bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pediatric Acute Myeloid Leukemia with Nucleophosmin Mutations Is Characterized by a Gene Expression Signature with Dysregulated HOX Gene Expression Distinct from MLL-Rearranged Leukemias.
Authors: Mullighan Charles G. , Kennedy Alyssa L. , Zhou Xiaodong , Shurtleff Sheila A. , Downing James R. 
Published: April 2020

Abstract
Recent studies have identified mutations in the nucleophosmin (NPM) gene in up to one-third of cases of acute myeloid leukemia (AML) lacking a recurring cytogenetic abnormality. NPM mutations (NPMm+) result in aberrant cytoplasmic localization of nucleophosmin, which may potentially perturb multiple cellular pathways including cell cycle regulation. However the exact mechanisms by which mutant NPM contributes to leukemogenesis are unclear. Gene expression analysis may identify mediators or pathways in NPMm+ AML that are important in the development of leukemia. We have examined NPM mutation status in a 93 cases of pediatric AML and correlated mutation status with gene expression profile. All major AML subgroups were studied including AML-ETO (n=18), MLL rearranged (n=14) CBFB-MYH11 (n=13), PML-RARA and variants (n=4), acute megakaryoblastic leukemia (n=4), and AML with normal cytogenetics (n=20), or non-recurring cytogenetic abnormalities (n=20). Exon 12 of NPM was PCR amplified, sequenced, and abnormal cases verified by cloning and sequencing. Gene expression profiling was performed using Affymetrix U133A arrays. Six cases with tetranucleotide insertion mutations in NPM exon 12 were identified. Four had normal cytogenetics, and two non-recurring cytogenetic abnormalities. Differential gene expression between NPMm+ and NPMm- AML (either all NPMm- cases, or only those NPMm- cases lacking recurring cytogenetic abnormalities) was assessed by t-test. NPMm+ AML was characterized by upregulation of multiple homeobox genes (e.g. HOXA9, A10, B2, B6) as well as multiple genes with known or potential roles in tumorigenesis, such as MEIS1 and the NPM fusion partner ALK. This pattern of disordered HOX expression is similar to that of MLL-rearranged leukemia; however comparison of the signatures of NPMm+ and MLL-rearranged leukemia identified important differences, such as upregulation of HOXB2, B3, B6 and D4 in NPMm+ AML but not MLL-leukemia. These results confirm a recently published report describing perturbed HOX expression in NPMm+ AML (Alcalay et al. Blood2005;106:899), and provide the first evidence that the NPMm+ signature is similar to but distinct from MLL-rearranged AML. These findings provide important insights into the pathogenesis of NPMm+ leukemia, and support the hypothesis that mutated NPM dysregulates HOX expression via a different mechanism than MLL rearrangement.
Gene Expression Profiles in Acute Myeloid Leukemia (AML): From Diagnosis to Prognosis.
Authors: Lee Sanggyu , Chen Jianjun , Zhou Goulin , Shi Run , Kocherginsky Masha , Karrison Theodore G. , Kim Yeong Cheol , Ge Xijin , Jayathilaka Nimanthi , Neilly Mary Beth , Bouffard Gerard , Young Alice , Kornblau Steven , Bloomfield Clara , Bohlander Stefan , Liu Pu Paul , Sun Miao , Wang San Ming , Rowley Janet D. 
Published: April 2020

Abstract
Chromosome translocations are among the most common genetic abnormalities in human leukemia. The abnormally expressed genes from each translocation can be used to identify specific markers for clinical diagnosis of each translocation. Microarrays have identified genes differentially expressed in different translocations but the results between laboratories are not always compatible. We used SAGE to quantitate gene expression in bone marrow(BM) samples from 22 patients with four types of AML, [de novo AML M2 with t(8;21), AML M3 or M3V with t(15;17), AML M4Eo with inv(16), AML M5 with t(9;11) or secondary t(9;11)].We made SAGE libraries from CD15+ leukemic myeloid progenitor cells, collecting over 106 SAGE tags, of which 209,486 were unique tags; 136,010 were known genes and ESTs, and 73,476 were novel transcripts. SAGE tags for further analysis were selected based on a 5-fold difference between patient’s samples and normal CD15+ BM; they were also statistically significantly different at the 5% level. Using these strict criteria, we identified 2,381 unique tags, of which 2,053 were known genes and ESTs, and 328 were novel transcripts that were either specific for each translocation or were common(55) SAGE tags for all 4 translocations. The major change in all translocations was a decrease in expression in leukemia cells compared with normal cells; the decrease was least in the t(8;21) cells. Changes in expression of these known genes, which fall into different gene ontology functional categories, varied by translocation. Those associated with macromolecular biosynthesis, transport and transcription were most altered in the t(8;21); those related to defense response and apoptosis were altered in the t(15;17); cell proliferation genes were most affected by the t(9;11). From this analysis, we identified the functional molecular signature of each translocation. We designed a custom microarray to validate our SAGE data analysis. Our initial microarray contained 349 probes including 212 known genes, 61 ESTs, 28 novel sequences based on our data and 48 genes reported by others. We have now included 65 additional probes that appeared to be correlated with survival. Using 63 samples with the four translocations [16 inv(16), 4 t(9;11), 20 t(15;17), 4 t(8;21) and 19 other translocations], we are validating which genes provide a robust, reproducible “fingerprint” for each translocation, for all translocations, and which ones provide reliable information related to prognosis and survival. Our results will provide new insights into genes that collaborate with each translocation to lead to a fully leukemic phenotype as well as which genes appear to provide valid prognostic information.
Initial Results of a Randomized, Prospective Trial of Prophylaxis To Prevent Joint Disease in Young Children with Factor VIII (FVIII) Deficiency.
Authors: Manco-Johnson Marilyn J. , Abshire Thomas C. , Brown Deborah , Buchanan George R. , Cohen Alan R. , DiMichele Donna , Hoots W. Keith , Leissinger Cindy A. , McRedmond Kevin , Nugent Diane J. , Shapiro Amy D. , Thomas Gregory A. , Valentino Leonard A. , Riske Brenda 
Published: April 2020

Abstract
Background: Retrospective reviews of hemophilia therapy correlate normal joint X-ray (XR) and physical exam (PE) with early institution of routine infusions of FVIII dosed to prevent bleeding. Although the National Hemophilia Foundation recommended prophylaxis for all persons with severe hemophilia in 1995, fewer than half of affected persons in the US have adopted prophylaxis due to cost, effort, lack of perceived need and complications.
Objective: The “Joint Outcome Study” was constructed as a multi-center, open-label, two-arm, prospective, randomized clinical trial to compare full prophylaxis with an intensive treatment regimen for joint hemorrhage.
Methods: A regimen of every other day infusions of FVIII at 25 U/kg to prevent hemorrhage (prophylaxis, P) was compared with intensive therapy using ≥ 3 infusions totaling ≥ 80 U/kg FVIII at the time of each joint hemorrhage to minimize joint damage (enhanced episodic, EE). Primary outcome was the proportion of boys in each arm with bone or cartilage damage on XR or magnetic resonance imaging (MR) of index joints (elbows, knees, and ankles). Outcomes were judged independently by two research radiologists who were blinded to treatment arm and bleed history, with a third for discrepant readings. Other outcomes included joint function on a physical exam scale validated for young children (PE), # of joint hemorrhages and factor utilization. Boys were followed from entry between 12 and 30 months until age 6 years. At entry all children had normal joints on XR and MR and had no more than two hemorrhages into any one joint.
Results: Sixty-five boys were randomized to P (32) or EE (33). The study has been completed. While adjudication of XR and MR outcomes is still ongoing, clinical study results show the following: Children on P consumed more FVIII (mean 163 vs 47 infusions/year, P &lt; 0.001) and had fewer joint hemorrhages per year (0.47 vs 4.9, p &lt; 0.001) than boys on EE. PE scores for the six index joints were lower on the P arm compared with EE (mean score 4.7 vs. 8.6, p&lt; 0.01).
Conclusion: This first randomized clinical trial of prophylaxis in young children with FVIII deficiency showed improved joint function by age 6 years in children on early every other day prophylaxis in comparison to an aggressive program of multiple infusions administered promptly at the time of joint hemorrhage. Joint structural outcome confirmation will be based on MR and XR.
MicroRNA Expression Profiling of Diffuse Large B-Cell Lymphoma Reveals Differences between Germinal Center-Like and Activated B Cell-Like Subtypes.
Authors: Lawrie Charles H. , Soneji Shamit , Cooper Christopher D. , Hatton Chris 
Published: April 2020

Abstract
MicroRNAs (miRNA) are a recently discovered class of short non-coding RNA molecules that negatively regulate gene expression. They have been shown to play a critical role in many biological functions. In humans about 320 miRNAs have been identified, some of which are expressed in a cell-specific and developmental stage-specific manner. Recently it has been shown that the expression profile of miRNAs can be used to subtype clinical cases (and cell lines) according to diagnosis with a greater degree of accuracy than traditional gene expression analysis. The identity of miRNAs associated with different lymphoma types however remains poorly defined. Previous expression studies have revealed the presence of at least two subtypes of diffuse large B-cell lymphoma (DLBCL) representing the postulated cell of origin; those that are germinal center B cell derived (GCB-type) and those that are activated B-cell derived (ABC-type). The latter subtype has been linked with poor prognostic outcome. It is not known whether these subtypes are also defined at the miRNA level. Therefore we examined the miRNA expression profile of DLBCL cell lines of defined subtypes as well as sub-populations of B-lymphocytes by microarray analysis. Consistent with recent publications, we found that mir-19a, 19b and 17-5p (part of mir-17-92 cluster) were up-regulated in cell lines but not in normal lymphocyte populations. Furthermore, cluster analysis showed that GCB-type cell lines (SUD-HL4, SUD-HL6 & SUD-HL10) have a distinct miRNA profile from ABC-type cell lines (OCI-Ly3 & OCI-Ly10). Most notably, high levels of expression of mir-155, mir-181b and mir-325 were found in ABC-type cell lines whilst high levels of mir-181a were found in GCB-type cell lines. We looked at expression of mir-155, 181a, 143, 145, 378 and 16 in these cell lines as well as clinical cases of DLBCL by RNase-protection assay. Consistent with the microarray data, we found that mir-155 was expressed in ABC-type cell lines but not GCB-type cell lines whilst the converse was true for mir-181a. Clinical cases showed similar patterns of expression but have still to be sub-typed according to immunohistochemical markers. Although still preliminary, our data suggests that miRNA profiling may be a useful tool in predicting the subtype of DLBCL cases and hence clinical outcome.
The MDS-Associated Protein EVI1 Impairs Erythroid and Megakaryocytic Differentiation by Direct Interaction with GATA-1.
Authors: Laricchia-Robbio Leopoldo , Li Donglan , Fazzina Raffaella , Chakraborty Soumen , Hay Maher Abdul , Nucifora Giuseppina 
Published: April 2020

Abstract
EVI1 is an aggressive nuclear oncoprotein deregulated by recurring chromosomal abnormalities in acute myeloid leukemia and myelodysplastic syndrome. This protein has two Zn finger domains containing 7 motifs at the N-terminus and 3 motifs at the C-terminus. The expression of this gene is a very poor prognostic marker and is associated with diseases characterized by erythroid and megakaryocytic defects. We have recently shown that the forced expression of EVI1 in murine bone marrow results in a fatal disease with features characteristic of MDS, including fatal dyserythropoiesis, dysmegakaryopoiesis, and anemia. These lineages are regulated by the transcription factor GATA-1, a DNA-binding protein that in addition to erythrocytes and megakaryocytes exerts a strict control also on the differentiation of mast cells and eosinophils, on the basis of its expression and association with specific partners.
In the present study, we used biochemical assays and in vitro culture to show that GATA-1 and the N-terminus of EVI1 are involved in the formation of a protein complex that is unable to regulate efficiently GATA-1-dependent promoters in reporter gene assays. EMSA studies with a GATA-1-specific probe indicate that EVI1 does not recognize and bind to the DNA probe but disrupts the DNA-binding of GATA-1. By deletion analysis and point mutations, we mapped the interaction between the proteins to two motifs in the proximal Zn finger domain of EVI1 and to the C-terminus Zn finger of GATA-1. Cys to Ala mutations in the two EVI1 motifs abrogate the interaction and restore the response of a promoter in reporter gene assays. We propose that the association between EVI1 and the DNA-binding motif of GATA-1 impairs efficient promoter binding by GATA-1 and the regulation of erythroid and megakaryocytic lineage. There studies suggest that the interaction surface between the two proteins could be an attractive target for the development of competing small molecules as a treatment in EVI1-associated leukemia.
Outcomes of Unrelated Cord Blood and Haploidentical Stem Cell Transplantation in Adults with Acute Leukaemia.
Authors: Rocha Vanderson , Aversa Franco , Labopin Myriam , Sanz Guillermo , Ciceri Fabio , Arcese William , Bunjes Donald , Rowe Jacob M. , Di Bartolomeo Paolo , Frassoni Francesco , Martelli Massimo F. , Gluckman Eliane 
Published: April 2020

Abstract
Unrelated cord blood transplantation (UCBT) and Haploidentical T-cell depleted peripheral blood stem cell transplantation (Haplo) are alternative options to treat patients with high risk acute leukaemia. With the aim to compare the outcomes of both strategies we have analysed retrospectively adults patients with ALL or AML receiving either UCBT or Haplo performed in EBMT centers from 1998–2002. One hundred forty four patients had ALL (Haplo=75 and UCBT=73) and 220 had de novo AML (Haplo=154, UCBT=66). In the ALL group, UCBT patients were younger and received less TBI than Haplo recipients. The frequency of patients with advanced phase of the disease at transplant was 45% in Haplo and 51% in UCBT (p=0.79). Cytogenetics and interval from diagnosis to transplant were not statistically different between the 2 groups. In the AML group, UCBT recipients were younger than Haplo recipients. Many patients were transplanted in advanced phase of the disease in both groups (58% of Haplo recipient and 59% in UCBT group), other disease-related factors were not significantly different. Unadjusted outcomes in both groups are reported in table 1.
After statistical adjustment for differences between the 2 groups, in both analysis (ALL and AML), UCBT recipients had delayed neutrophil recovery and higher incidence of acute GVHD (II–IV) compared to Haplo recipients. In the AML group, relapse incidence, TRM and LFS were not statistically different after UCBT or Haplo, however in ALL group, LFS were superior and relapse incidence decreased after UCBT compared to Haplo transplants. In conclusion, in this based registry retrospective analysis, UCBT and Haplo showed similar TRM, relapse and LFS for adults with AML, however LFS were superior after UCBT for patients with ALL due to decreased incidence of relapse.
ALL Cumulative incidence of aGvHD Cumulative incidence of 2y-RI Cumulative incidence of 2y-TRM Kaplan Meyer estimate 2y-LFS Haplo (n=75) 8+/−3% 38+/−5% 49+/−6% 13+/−4% UCBT (n=73) 26+/−5% 23+/−4% 41+/−6% 36+/−6% p value 0.004 0.07 0.55 0.01 AML Haplo (n=154) 5+/−5% 18+/−3% 58+/−4% 24+/−4% UCBT (n=66) 23+/−5% 24+/−5% 46+/−2% 30+/−6% p value &lt;0.0001 0.44 0.23 0.39
A microRNA Cluster as a Target of Genomic Amplification in B-Cell Lymphomas.
Authors: Tagawa Hiroyuki , Karbe Kennosuke , Ohshima Koichi , Morishima Yasuo , Nakamura Shigeo , Seto Masao 
Published: April 2020

Abstract
Background: Genomic gain/amplification of 13q31-q32 is frequently observed in malignant lymphomas. C13orf25, recently established as a candidate gene in malignant lymphoma via 13q31-q32 genomic amplification, encodes two variant transcripts by alternative splicing (Ota et al, Cancer Res 2004). Seven microRNA genes (miR-17-5p, miR-17-3p, miR-18, miR-19a, miR-19b, miR-20 and miR-92) are clustered in C13orf25 transcript variant 2 (C13orf25 v2). Because microRNAs display dynamic temporal and spatial expression patterns, disruption of these microRNAs may be associated with tumorigenesis.
Purpose: The purposes of this study are i) to reveal frequencies of the 13q gain/amplification in various lymphoma types, and ii) to examine the expression of C13orf25 v2 and seven microRNAs using various lymphoma cell lines and tumors with and without 13q gain/amplification.
Experimental Design: We analyzed genomic alterations of chromosome 13 for 12 malignant lymphoma cell lines (eight B-cell and four T-cell lymphomas), and 214 cases of B-cell lymphomas (136 cases of diffuse large B-cell lymphoma (DLBCL), 27 cases of sporadic Burkitt’s lymphoma (sBL), 29 of mantle cell lymphoma (MCL), 22 of follicular lymphoma (FCL)) and 20 cases of T-cell lymphoma by using array-based comparative genomic hybridization. The expression levels of seven microRNAs using 12 lymphoma cell lines with (four) and without (eight) 13q gain/amplification were examined by Northern-blot and quantitative real-time PCR (RQ-PCR) analyses. RQ-PCR for C13orf25 v2 (microRNA cluster) was also conducted for 21 cases of DLBCL (eight cases with 13q gain/13 cases without), 10 cases of sBL (four cases with 13q gain/amp/six cases without) and 10 cases of mantle cell lymphoma.
Results: Frequent (&gt; 20%) gain/amplification of 13q were detected in DLBCL (31 cases, 23%) and Burkitt’s lymphoma (8 cases, 30%) but no gain/amplification at 13q was found in MCL, FCL and T-cell lymphomas. Genomic amplification of 13q31-q32 was observed in four cases of DLBCL and two cases of sBL, four of which were c-MYC rearranged (two cases of DLBCL and two cases of sBL). RQ-PCR and Northern blot analyses revealed that five of the seven mature microRNAs displayed overexpression in lymphoma cell lines with 13q31 genomic gain/amplification but not in those without. RQ-PCR analysis for 21 cases of DLBCL demonstrated that the cases with 13q gain/amplification (8 cases) showed significantly higher expression of C13orf25 v2 than those without (13 cases) (Mann Whitney U test, P &lt; 0.05). Significant higher levels of the five microRNAs in sBL with 13q gain/amplification were also confirmed by Northern blot analysis. Lower expression levels of the microRNAs were found in T cell lymphoma cell lines and tumors.
Conclusion: These results suggest that the microRNA cluster (C13orf25 v2) is a target of 13q/13q31 genomic gain/amplification in DLBCL and sBL.
Isolation of Cytomegalovirus (CMV) Specific T-Cells from Sersopositve Donors: A Possible Tool for CMV-Prophylaxis.
Authors: Borchers Sylvia , Topp Max , Ganser Arnold , Einsele Hermann , Weissinger Eva M. , Hertenstein Bernd 
Published: April 2020

Abstract
Reactivation of endogenous viruses, e. g. CMV, is a major cause of morbidity and mortality after allogeneic hemopoietic stem cell transplantation (allo-HSCT). Risk factors for the reactivation of CMV include the conditioning and immunosuppressive regimen, T-cell depletion of the graft, the development, and the treatment of acute or chronic graft versus host disease (GvHD). T-cells play an important role in the control of viral reactivation, lack of T-cells often leads to recurrent viral infections. The cytokine secretion assay provides the possibility to screen for CMV-reactive cells in a simple FACS assay by detection of interferon-gamma (IFN-gamma) secreting T-cells after stimulation of the cells with CMV-antigen. In addition IFN-g secreting cells can be enriched using the same assy. We have recently optimized enrichment to achieve 80-95% purity of IFN-gamma secreting T-cells.
In order to further optimize stimulation, several CMV-antigens were tested: While viral lysate provides a broad activation of CMV-specific T-cells, recombinant proteins like pp65 may offer more reproducible conditions. Comparison of viral lysate to pp65 regarding activation and enrichment of CMV-specific T-cells showed a possible HLA-dependency of pp65-performance: in HLA-A2-positve donor’s stimulation by pp65 was equal to stimulation with lysate, while in other donors pp65 was less effective. Interestingly, stimulation with lysate yielded mainly CD4-positive T-cells, whereas stimulation with pp65 mainly yielded CD8-positive T-cells.
Five patients, who reactivated CMV after allo-HSCT, were monitored closely for CMV-reactive cells to date. Initially all patients had no or reduced numbers of CMV-reactive T-cells. After one year, in 4 patients CMV-responsiveness was restored, none of these reactivated CMV more than twice. One patient had recurrent CMV-reactivations after HSCT, starting as early as day +20 after HSCT despite of GCV-treatment. Thus, CMV-specific enriched donor T-cells were transfused to control the reactivation. In an effort to minimize the risk of GvHD and to maximize protection from CMV-disease after allo-HSCT, we applied immunomagnetic selection for the isolation of CMV-reactive T-cells from the sero-positive donor. The persistence and proliferation of the transfused CMV-specific T-cells was monitored. During the first 4 weeks the percentage of CMV-reactive T-cells raised from undetectable levels to 3.5%, while CMV-antigenemia declined. After 3 weeks a complete clearance of CMV was achieved. No GvHD occurred, despite a mismatch in HLA-DR between donor and recipient. These preliminary data suggest the feasibility and safety of the transfusion of CMV-specific T-cells after immunomagnetic selection for the treatment of CMV-reactivation.