1,721,045 research outputs found
In search of the original leukemic clone in chronic myeloid leukemia patients in complete molecular remission after stem cell transplantation or imatinib
No full textIt is not clear if absence of BCR-ABL transcripts - complete molecular response (CMR) - is synonymous with, or required for, cure of chronic myeloid leukemia (CML). Some patients achieve CMR with imatinib (IM), but most relapse shortly after treatment discontinuation. Furthermore, most patients in long-term remission (LTR) post stem cell transplantation (SCT) are considered 'functionally cured', although some remain occasionally positive for low level BCR-ABL mRNA. Interpretation of the latter is complicated since it has been observed in healthy individuals. We designed a patient-specific, highly sensitive, DNA quantitative PCR to test follow-up samples for the original leukemic clone, identified by its unique genomic BCR-ABL fusion (gBCR-ABL). In 5 IM-treated patients in CMR, gBCR-ABL was detected in transcript-negative samples; 4 patients became gBCR-ABL-negative with continuing IM therapy. In contrast, out of 9 patients in LTR (13-27 years) post-SCT, gBCR-ABL was detected in only 1, despite occasional transcript-positive samples in 8 of them. In conclusion, in IM-treated patients, absence of transcripts should not be interpreted as absence of the leukemic clone, although continuing IM after achievement of CMR may lead to further reduction of residual disease. Post-SCT, we found little evidence that the transcripts occasionally detected originate from the leukemic clone
How cured are CML patients in complete molecular remission (CMR) after stem cell transplantation or imatinib?
No full textIt is unclear if CMR, i.e., absence of BCR-ABL mRNA, is synonymous with, or even required for, cure of chronic myeloid leukemia (CML). This is particularly relevant for management of the minority of patients who achieve CMR with imatinib (IM). Although most patients in long-term remission (LTR) post-stem cell transplantation (SCT) are considered "functionally cured", BCR-ABL mRNA is occasionally detected in their peripheral blood (PB), at a level similar to that detectable in the PB of healthy individuals. Most CML patients in CMR on IM relapse shortly after treatment discontinuation. We sought to elucidate the quality of the molecular response in these two groups of CML patients by using a genomic DNA (gDNA) real-time quantitative PCR (RQ-PCR) with patient-specific primers/probe combinations for detection of BCR-ABL genomic fusions (gBCR-ABL). gBCR-ABL - a molecular signature of each CML case - was sequenced from pre-SCT or pre-/early-IM therapy using inverse PCR (I-PCR) or long-range genomic PCR (LR-PCR). The I-PCR involved digestion of gDNA with RsaI, circularization of the fragments, and amplification with 2 sets of inverse primers located in the 5' end of the RsaI-fragments of the major breakpoint region of BCR for cloning and sequencing of the BCR-ABL band. The LR-PCR is a multiplex reaction with forward primers on BCR exons 13 or 14, and 20 reverse primers, spanning 150kb of the ABL breakpoint region. The patient-specific products are then directly sequenced. Knowledge of the sequence allowed us to design patient-specific primers/probe combinations that were then used to test gDNA from PB follow-up (FU) samples using novel single-step or nested RQ-PCR assays. When tested in serial dilutions of the sample from which the breakpoint sequence was obtained, both methods generated standard curves of similarly good quality; the nested approach did not improve the sensitivity of the assay, with both methods being capable of detecting one single target DNA molecule per reaction. The specifity of the assay was demonstrated using at least 2 different BCR-ABL-positive gDNAs and a no-gDNA negative controls, whereas the sensitivity was maximized by testing a minimum of 7.2µg gDNA in multiple reactions. From 6 patients in LTR post-SCT (median time post-SCT 186 months; range: 87 to 333) we tested 9 FU samples collected between 87 and 321 months post-SCT (median: 168). From 3 IM-treated patients we tested 5 samples in CMR collected between 36 and 75 months (median: 63) after the start of IM. Six of the 9 post-SCT samples had been classified as low-level positive for BCR-ABL transcripts (BCR-ABL/ABL 0.001 to 0.012%): only 1 was positive for gBCR-ABL (BCR-ABL/ABL from this sample - 0.003%). Of the 3 patients in CMR on IM, 1 had 1 sample negative for gBCR-ABL; 1 had 1 sample positive and 1 sample negative 37 months later; 1 had 2 positive samples separated by 36 months. The FU samples positive for gBCR-ABL were positive at a very low level, with only 1 or 2 positive reactions out of a minimum of 24 replicates, with Ct values very close to the threshold of detection of the standard curves. In conclusion, the results so far suggest that, in post-SCT patients in LTR, the original BCR-ABL positive clone is rarely detected, and in most instances may not be the cause of low-level positivity for BCR-ABL mRNA. The leukemic clone may be more frequently present in IM-treated patients in CMR, which suggests the need for continuing IM even after achievement of CMR
Array CGH analysis at 60kb resolution of CML samples at advanced stage of disease
No full textIn spite of the universal presence of the BCR/ABL1 fusion gene, chronic myelogenous leukemia (CML) shows remarkable clinical and genetic diversity. The consequences of der(9)t(9;22) chromosome deletions, associated with poor survival, as well as the mechanism behind their formation remain unclear, as does our understanding of the molecular events driving the disease evolution. The presence of these deletions fuelled the expectations that cryptic genome-wide aberrations may be accountable for the disease progression. Following a comprehensive BAC aCGH analysis of 48 CML samples (Brazma et al., Genes, Chromosomes & Cancer, 2007 in press) we report high-resolution oligo-nucleotide array study of a further 30 CML accelerated/ blast phase samples. We were unable to confirm the high frequency of particular single BAC imbalances (CNVs), reported both by ourselves and others, possibly due to the manufacturer’s array selection strategy. Never-the-less some of the CNVs and a wealth of new imbalances were obtained at 60kb resolution. It was possible to build a precise map of the amplicon affecting the sequences flanking the 3' ABL1 breakpoint site, which include the LAMC3 and NUP214 genes. The presence of this amplicon was associated with therapy resistance. When assessed, at a resolution of 60 kb, the deletions of the regions flanking the ABL1/BCR breakpoint showed novel features:
1. the genome loss affects preferentially both flanking sites as seen in 5 of the 6 ‘deleted’ samples and 2. the 120kb deletion identified is the smallest recorded so far. Most of the major cytogenetic features of the samples were confirmed and a number of cryptic genome imbalances were detected, from 120kb to 10Mb in size, involving regions rich in genes, some already implicated in the pathogenesis of CML. Finally, recurrent micro aberrations of several adjacent oligo-nucleotides affecting non-coding sequences were detected in as many as 2/3 of the samples
The platelet-derived growth factor receptor beta fuses to two distinct loci at 3p21 in imatinib responsive chronic eosinophilic leukemia
No full textWe have identified three patients (2 adults, one infant) who presented with BCR-ABL negative eosinophilic myeloproliferative disorders. Cytogenetic analysis revealed a t(1;3;5)(p36;p21;q33) for case 1 and a t(3;5)(p21–25;q31–35) for cases 2 and 3. Two-color fluorescence in situ hybridization (FISH) using differentially labelled probes flanking PDGFRB indicated that this gene was disrupted in all three cases. 5' rapid amplification of cDNA ends (5'RACE) for case 1 identified an in-frame mRNA fusion of exon 9 of the WDR48 gene at 3p21 to exon 12 of PDGFRB. The chimeric mRNA is predicted to encode a 872 amino acid fusion protein that retains the amino terminal WD repeat region of WDR48 fused to the transmembrane and intracellular tyrosine kinase domains of PDGFRbeta. Cases 2 and 3 were negative for the WDR48-PDGFRB fusion mRNA by RT-PCR using several combinations of primers. 5'RACE PCR from case 2 RNA identified a fusion involving a second 3p21 gene: GOLGA4 exon 11 was fused in-frame to exon 11 of PDGFRB. Exactly the same fusion was found in case 3. The predicted 991 amino acid protein included the amino terminal coiled-coil domain of GOLGA4 fused to the transmembrane and intracellular tyrosine kinase domains of PDGFRbeta. Interestingly, both WDR48 and GOLGA4 are involved in endocytic shuttling pathways. The presence of all fusions was confirmed by RT-PCR and identification of the genomic breakpoints. Imatinib, a known inhibitor of PDGFRbeta, selectively blocked the growth of patient CFU-GM for case 2. Following the identification of PDGFRB rearrangements, all three patients were treated with imatinib. Case 1 was in transformation, but responded rapidly to minimal doses of imatinib (800mg daily for 4 days) with complete cytogenetic remission but remained pancytopenic. Blast crisis recurred 8 months later, responded similarly to 3 days of imatinib, but the patient died 2 months later of invasive fungal infection. Case 2 responded clinically and remains in sustained cytogenetic and molecular remission (nested RT-PCR negative for GOLGA4-PDGFRB). Case 3 (a 13 month old boy) had a complete hematologic response to 50mg/day imatinib but the t(3;5) was still seen in 40% of metaphases at 3 months. We conclude that PDGFRB fuses to diverse partner genes to give rise to atypical MPDs. Although very rare, identification of these fusions is critical for proper management of affected individuals
ST1571 (Imatinib Mesylate) reduces bone marrow cellularity and normalizes morphologic features irrespective of cytogenetic response
No full textThe tyrosine kinase inhibitor STI571 (imatinib mesylate, Gleevec) is an effective treatment for chronic myeloid leukemia (CML). We examined bone marrow samples from 53 patients with CML who were receiving STI571 in 3 multicenter phase 2 trials to assess morphologic changes and cytogenetic response to this drug. In most patients with initially increased blasts, the bone marrow blast count rapidly decreased during STI571 therapy. Reductions in cellularity, the myeloid/erythroid ratio (commonly with relative erythroid hyperplasia), and reticulin fibrosis (if present pretreatment) also were seen in most patients, resulting in an appearance resembling normal marrow in many cases. Eighteen patients (34%) had some degree of cytogenetic response. Surprisingly, these striking morphologic changes occurred irrespective of any cytogenetic response to STI571. Thus, STI571 seems to affect the differentiation of CML cells in vivo, causing even extensively Philadelphia chromosome-positive hematopoiesis to exhibit features resembling normal hematopoiesis. <br/
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Reduced-intensity conditioning for myeloma: lower nonrelapse mortality but higher relapse rates compared with myeloablative conditioning
No full text: Despite the widespread adoption of reduced-intensity conditioning (RIC) for myeloma, there are few data comparing outcomes with RIC with myeloablative conditioning (MAC). We report the outcomes of patients undergoing allogeneic transplantations for myeloma and reported to the EBMT. A minimum data set was available on 320 RIC and 196 MAC allografts performed between 1998 and 2002. The RIC patients were older (51 vs 45 years) with more progressive disease (28% vs 21%) and more had received a prior transplant (76% vs 11%). In addition, there was a longer time to transplantation and an increased use of peripheral blood and T-cell depletion. For RIC and MAC, respectively, the nonrelapse mortality (NRM) at 2 years was 24% and 37% (P = .002); overall survival, 38.1% and 50.8% (not significant [ns]); and progression-free survival (PFS), 18.9% and 34.5% (P = .001). On multivariate analysis, RIC was associated with a reduction in NRM (HR, 0.5), but this was offset by an increase in relapse risk (HR, 2.0), and the conditioning intensity did not impact on overall survival or retain significance for PFS. These data suggest that there is a continuing need to investigate dose intensity in the conditioning for myeloma allografts
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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