bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel Molecular and Immunological Monitoring of Minimal Residual Disease in Adult Acute Lymphoblastic Leukemia (ALL) Patients.
Authors: Parovichnikova E.N. , Davidyan J.R. , Galtzeva I.V. , Surin V.L. , Vorobiev I.A. , Gretzov E.A. , Isaev V.G. , Savchenko V.G. 
Published: October 2019

Abstract
Though the initial response to induction therapy, indicating rapid tumor clearance, is currently considered to be one of the most important prognostic factors, detection of submicroscopic levels of minimal residual disease (MRD), by means of PCR or immunophenotyping after induction and during different stages of treatment, has also become important in predicting outcome in ALL patients. We initiated a study using parallel PCR and flow cytometry to monitor MRD in adult acute lymphoblastic leukemia (ALL) patients treated by standard approach. Bone marrow samples were analyzed at diagnosis, after pre-phase (one week of steroid therapy to determine steroid responsiveness), at 8-weeks post induction, at consolidation, before maintenance (+7–8 mo), and during maintenance for the detection of clonal IgH, TCR-gamma rearrangements by PCR (The level of detection sensitivity is 10−3 to 10−4). Specific markers were identified for 88% of the patients (30/34); prolonged monitoring was carried out in 22 patients with follow up from 2 to 24 months. Fifteen of those patients were analyzed by three-color flow cytometry analysis with a panel of 20 monoclonal antibodies for patient-specific aberrant leukemia-associated phenotype (LAP) at diagnosis and before maintenance (10−4). Contrary to PCR analysis, LAPs were detected in all patients. The most common LAPs were CD19/34/10, CD 19/34/TdT, and CD19/34/IgM. Clinical CR was achieved in 85% of patients. Prednisone resistance was detected in 71% of patients. MRD was detected by PCR in all patients after pre-phase, in 21/22 (95%) after 1st induction phase, in 11/15 (73%) after 2nd induction phase, in 10/15 (67%) after consolidation, and in 8/14 (57%) before maintenance. Flow cytometry data coincides with molecular parameters: only 4 of 10 patients examined before maintenance (+7–8 mo) had no cells with LAP. Comparing our parallel measurements we have noted discrepancies in 3 of 10 cases. Two immunologically positive patients were PCR-negative, and one PCR-positive patient was immunologically negative.
All patients (n=3) whose PCR probes were positive more than twice, relapsed at different time points; no relapses were noted in once positive patients (n=3), and 1of 8 PCR-negative patients relapsed. Our data indicate that both methods are effective and relevant in detection of MRD. They show very slow tumor clearance in ALL patients. MRD positivity reflects the higher relapse probability. More patients can be followed for MRD with flow-cytometry, due to higher detection rate of LAP.
A FLT3 Gene-Expression Signature Outperforms FLT3 Status in Predicting Clinical Outcome for Patients with Normal Karyotype AML.
Authors: Bullinger Lars , Dohner Konstanze , Stirner Christoph , Rucker Frank G. , Frohling Stefan , Kim Young H. , Schlenk Richard F. , Tibshirani Robert , Dohner Hartmut , Pollack Jonathan R. 
Published: October 2019

Abstract
In acute myeloid leukemia (AML), cyotgenetics is used to stratify cases for appropriate risk-adapted therapy. The largest subset of patients, those with normal karyotype AML (NK-AML), comprises a heterogeneous group with intermediate prognosis. To improve outcome prediction for this group, we carried out gene-expression profiling of a set of 65 clinically-annotated NK-AML cases. In exploratory studies, an outcome predictor derived from semi-supervised analysis comprised genes mainly correlated with the presence of FLT3 (fms-related tyrosine kinase 3) internal tandem duplication (ITD) activating mutation, itself a prognostic factor. We therefore sought to directly define and characterize a gene-expression predictor of FLT3-ITD mutation status. Using a supervised analysis (Prediction Analysis of Microarrays), we identified an optimal 25-gene FLT3 signature, which in an independent set of 73 NK-AML cases was a significant predictor of clinical outcome, notably outperforming FLT3-ITD mutation status itself. We speculate that the signature identifies cases with alternative genetic or epigenetic changes that phenocopy FLT3-ITD, and the signature genes provide a starting point to dissect these pathways. Our findings underscore the prognostic relevance of FLT3-ITD in NK-AML, and indicate the potential clinical utility of a gene-expression based measure of clinically-relevant FLT3 pathway activation.
Diagnostic and Prognostic Significance of Tryptase in Clinical Hematology: A Single Center Experience from 1070 Patients.
Authors: Sperr Wolfgang R. , El-Samahi Aischa , Girschikofsky Michael , Winkler Stefan , Semper Hans , Agis Hermine , Sillaber Christian , Endler Georg , Rumpold Helmut , Lutz Dieter , Valent Peter 
Published: October 2019

Abstract
Recent data suggest that tryptase is expressed in neoplastic cells in various myeloid neoplasms. In this study, serum tryptase levels were determined by a fluoroenzyme-immunoassay in 165 healthy subjects, in 925 patients (pts) with hematologic malignancies (myeloproliferative disorders, MPD, n=150; myelodysplastic syndromes, MDS, n=233; acute myeloid leukemia, AML, n=317; acute lymphatic leukemia, ALL, n=26, Non Hodgkin′s lymphomas, NHL, n=30; systemic mastocytosis, SM, n=89), and in a large cohort of control cases (pregnant women, n=11; hepathopathy, n=7; renal failure, n=18; helminth infections, n=29; reactive leukocytosis/thrombocytosis or idiopathic cytopenia, n=115). In healthy subjects, the 95%-percentile ranged between 2.4 and 9.5 ng/ml (median 5.7 ng/ml). Healthy controls aged ≤ 16 years had a slightly lower median serum tryptase level compared to older control subjects (p=0.03). Among pts with non hematologic disorders, slightly elevated serum tryptase levels (up to 24 ng/ml) were detectable in 6/18 pts with severe renal failure and in 3/29 pts with helminth infections. When analyzing hematologic malignancies, tryptase levels >15 ng/ml could be detected in pts with myeloid neoplasms exclusively, whereas in most pts with lymphoproliferative disorders, tryptase levels were normal. Among myeloid neoplasms, elevated tryptase levels were recorded in 83% of the pts with SM, 36% of pts with AML, 34% of the pts with CML, and 29% of the pts with MDS. The highest tryptase levels, sometimes exceeding 1000 ng/ml, were found in pts with SM or AML-M4eo. In pts with CML, elevated tryptase levels were found to be associated with an unfavorable prognosis concerning survival (survival in CML pts with tryptase <15 ng/ml: 100% vs 71% in those with >15 ng/ml, after 60 months, p<0.007). In most pts with AML, SM, or CML, the initially enhanced serum tryptase levels decreased in response to successful cytoreductive or targeted therapy. In pts with AML, a persistently elevated serum tryptase in complete hematologic remission (CR) was found to be associated with an increased risk of relapse compared to those with normal tryptase in CR. In summary, tryptase is a new and simple diagnostic marker of myeloid neoplasms. In SM, AML, and CML, tryptase is also a useful marker to monitor (minimal residual) disease during treatment with cytoreductive or targeted drugs. Moreover, in AML and CML, measurement of tryptase is of prognostic significance. All in all, tryptase is recommended as a new important serum-marker in clinical hematology.
Artificial Neural Network Analysis of HOX Gene Expression Profiles Predicts Prognostic Subgroups in Acute Myeloid Leukemia.
Authors: Finnegan Damian P.J. , Quinn Michael F. , Humphreys Mervyn , Lappin Terence R.J. , McMullin Mary Frances , Thompson Alexander , Ball Graham R. 
Published: October 2019

Abstract
The acute myeloid leukemias (AMLs) are a heterogeneous group of hematological malignancies with diverse clinical outcomes. Pre-treatment karyotype analysis identifies biologically distinct subgroups and is currently used as a predictor of response to induction chemotherapy and risk of relapse. Cases may be stratified into one of three prognostic groups as follows: relatively favorable prognosis [t(8;21), t(15;17) and inv(16)]; adverse prognosis [−5/del(5q), −7, abnormalities of chromosome 3q and complex karyotype]; and intermediate prognosis [remainder including normal karyotype]. HOX genes encode master transcription factors which regulate key developmental processes including differentiation, proliferation and apoptosis. Humans have 39 HOX genes and multiple lines of evidence implicate their deregulated expression in the pathogenesis of AML. Drabkin et al. (Leukemia2002; 16: 186–95) have reported that AMLs with a relatively favorable prognostic karyotype are associated with low levels of HOX gene expression whereas AMLs with an adverse prognostic karyotype have higher levels of expression. To further characterize HOX gene expression in cytogenetic prognostic groups we determined the expression profiles of 26 HOX genes by real-time quantitative PCR (Q-PCR) in diagnostic samples, representative of the three prognostic groups, from 26 patients with de novo AML. Profiles were then analyzed using Artificial Neural Network based computational approaches to identify a subset of HOX genes which could discriminate between prognostic groups in a predictive fashion. Predictive models were developed for each prognostic group. Predictive classification performance for prognostic groups based on blind data of 88%, 92%, and 97% (with equal sensitivity and specificity) were achieved for the three prognostic groups. The models were interrogated to determine the nature of the relationship between the key HOX genes identified and prognostic group. The relatively favorable prognosis group was primarily defined by downregulation of HOXA5 and upregulation of HOXC4. The intermediate prognosis group was characterized by upregulation of HOXB3 and downregulation of HOXD10 and the adverse prognosis group by downregulation of both HOXC5 and HOXD3. Although the sample size is small, the results show that Artificial Neural Network based computational approaches are capable of further characterizing HOX gene expression within AML prognostic groups as determined by presenting karyotype and that measuring the expression levels of a small number of HOX genes at diagnosis can provide useful clinical information in cases where karyotype analysis has been unsuccessful.
Prognostic Implications of the Immunophenotype in Biphenotypic Acute Leukemia.
Authors: Lee Je-Hwan , Min Yoo-Hong , Chung Chul Won , Kim Byoung Kook , Yoon Hwi-Joong , Jo Deog-Yeon , Shin Ho-Jin , Bang Soo-Mee , Won Jong-Ho , Zang Dae Young , Kim Hyeoung Joon , Chi Hyun-Sook , Lee Kyoo Hyung , Cheong June-Won , Kim Jin Seok , Kim Sun-Hee , Park Seonyang , Park Su Yon , Chung Jooseop , Lee Jae-Hoon , Park Chan-Jeoung 
Published: October 2019

Abstract
Biphenotypic acute leukemia (BAL) is a rare yet defined type of acute leukemia. We investigated the incidence, clinicopathologic characteristics, and clinical outcomes of BAL in Korean adults. The present study retrospectively analyzed clinicopathological and clinical data from 43 adult patients with BAL, defined using the EGIL scoring system, from 11 Korean institutes. The incidence of BAL was 2.1% among acute leukemias; 2.3% in male and 1.9% in female. Median age of 43 BAL patients, 25 males and 18 females, was 38 years (range, 16–74). The immunophenotype was myeloid/B-lymphoid (M+B) in 31 (72.1%), myeloid/T-lymphoid (M+T) in 10 (23.3%), and B/T-lymphoid (B+T) and myeloid/B/T-lymphoid (M+B+T) in one (2.3%) each. 37 patients had the results of cytogenetic analyses and Ph chromosome (n=14, 37.8%) was the single most common abnormal finding. Intensive induction chemotherapy was given in 36 of 43 patients: AML-type in 13 (36.1%), ALL-type in 8 (22.2%), and combined type in 15 (41.7%). Complete remission (CR) was induced in 29 patients (80.6%). The CR rate was significantly lower in M+T (5 of 9, 55.6%) than M+B (22 of 25, 88.0%) (P=0.039). Other unfavorable factors for CR were absence of CD19 (P=0.029) or CD20 (P=0.046), and presence of CD2 (P=0.040). The CR rates were not significantly different according to cytogenetic finding or type of induction chemotherapy. After median follow-up duration of 712 days among surviving patients, 11 patients relapsed with median relapse-free survival (RFS) of 3.08 years and 4-y RFS of 38.3% and 18 patients died with median overall survival (OS) of 2.49 years and 4-y OS of 30.1%. Multivariate analysis showed that high leukocyte counts (≥ 30,000/μl) at diagnosis (OR, 5.922; 95% CI, 1.379–25.429; P=0.017) was an independent unfavorable prognostic factor for RFS, and high leukocyte counts at diagnosis (OR, 9.348; 95% CI, 3.014–28.993; P<0.001) and M+T phenotype (OR, 3.259; 95% CI, 1.136–9.344; P=0.028) were independent unfavorable prognostic factors for OS. In summary, BAL was found in 2.1% of adult acute leukemias and M+T phenotype showed significantly poorer response to induction chemotherapy and inferior overall survival compared to M+B phenotype.
Hypomethylation Induction and Molecular Response after Decitabine Therapy in Chronic Myelomonocytic Leukemia (CMML).
Authors: Oki Yasuhiro , Jelinek Jaroslav , Kantarjian Hagop M. , Issa Jean-Pierre J. 
Published: October 2019

Abstract
Decitabine has shown therapeutic activity in patients with MDS and CMML. The mechanisms of response to therapy remain incompletely understood. In particular, the relative contribution of this drug’s ability to induce hypomethylation and cytotoxicity remains unclear. To address this issue, we studied the dynamics of neoplastic cell clearance during decitabine treatment determined by quantitative monitoring of the mutant allele using pyrosequencing. DNA extracted from peripheral blood mononuclear cells from consented patients with CMML in a decitabine phase II study were first screened for JAK2 and NPM1 mutations as previously reported. We identified three patients with mutations (two with JAK2 mutation, one with NPM1 mutation) and samples at multiple points during therapy were available. All three carried normal karyotype. LINE repetitive element methylation and several other gene specific methylations were also assessed. In the three patients, LINE methylation decreased after each cycle of therapy, and recovered to near baseline after the drug was stopped (e.g. during the first cycle, average relative hypomethylation from baseline was 13.9% at day 12 and 6.5% at day 28). At the same time, the proportion of circulating neoplastic cells decreased slowly after the first cycle (decrease by 19.3% at day 12 and 13.5% at day 28). A substantial decrease in mutant allele percentage was observed after cycles 2, 3, and 2 in patients 1, 2, and 3, respectively. Clinical complete responses were achieved along with molecular responses at cycles 5, 4 and 2, respectively. Patients 1 and 2 showed complete disappearance of detectable neoplastic clones, and had sustained remissions (duration 1.5 and 2.5 years). In patient 3, the proportion of neoplastic cells was lower than baseline but still detectable at clinical remission, and the remission only lasted 8 months. We conclude that neoplastic cell clearance after decitabine therapy in CMML is observed after several courses of therapy, and is initially seen concurrently with hypomethylation. While LINE methylation returns to its steady state values after completion of decitabine infusion, the tumor elimination process slowly continues. Our data suggest a non-cytotoxic mechanism of action for the drug, whereby the biology of the neoplastic clone is altered by hypomethylation, leading to delayed clearances of unknown mechanism. Possibilities include an immune response and effects on the neoplastic (or normal) stem cells.
Figure Figure
Circulating CD52 and CD20 Levels Predict for Progression and Survival in Patients with CLL Treated with Fludarabine (F), Cyclophosphamide (C), and Rituximab (FCR).
Authors: Alatrash Gheath , Keating Michael J. , O’Brien Susan , Wang Xuemei , Manshouri Taghi , Faderl Stefan , Ferrajoli Alessadra , Kantarjian Hagop M. , Lerner Susan , Wierda William G. 
Published: October 2019

Abstract
The CD52 and CD20 antigens are ubiquitously expressed on CLL B cells and are important therapeutic targets for the monoclonal antibodies alemtuzumab and rituximab, respectively. Circulating soluble CD52 (sCD52) and CD20 (sCD20) have been shown to have prognostic value in CLL, non-Hodgkin’s lymphoma and Hodgkin’s disease (Blood101:2507, 2003; Br J Haem123:850, 2003). The pharmacokinetics and therapeutic efficacy of these mAbs may be adversely affected by circulating sCD52 and sCD20. Using the previously described ELISAs, we measured levels of sCD52 and sCD20 at various time points in blood (PB) and bone marrow (BM) of chemotherapy-naïve patients treated with FCR. Treatment consisted of fludarabine 25 mg/m2 d1-3, cyclophosphamide 250mg/m2 d1-3, and rituximab 375–500mg/m2 d1 as previously described (JCO23:4079, 2005). Courses were repeated every 4 weeks for a total of 6 courses. Univariate and multivariate Cox proportional hazards models were fit to evaluate the correlations of sCD52 and sCD20 and baseline characteristics with progression free survival (PFS) and overall survival (OS). A total of 291 patients were included, pretreatment characteristics [median (range)] were as follows: age=57yrs (17–86); WBC=76.9K/μL(2.1–619.5); ALC=66.7K/μL(0.8–558); HGB=12.4g/dL(6.1–18.7); PLT=155K/μL(8–406); ß2M= 3.7mg/L(1.6–16.4); LDH=550 IU/L(103–1828). Patients with Rai stage 0=8; I–II=186; and III–IV=97. The median follow-up time for all patients is 56 months. Of the 278 responding patients, 88 (31.7%) have progressed; the median time to progression has not been reached. To date, the median survival time for the 291 patients has not been reached; 57 (19.6%) patients have died. Pretreatment characteristics analyzed included age, gender, PS, WBC, ALC, HGB, PLT, ß2M, and RAI stage; post-treatment factors included PCR for IgVH in BM, and sCD52 and sCD20 (BM and PB) levels at response. Univariate analyses identified the following predictors for PFS (p < .05): age, HGB, ß2M, PCR for IgVH at response, and PB sCD20 at response. Independent predictors for PFS identified in multivariate analysis included PCR for IgVH and PB sCD20 level at response. For OS, significant (p < .05) factors in univariate analyses included: age, HGB, ß2M, PCR for IgVH at response, and BM sCD52 at response. Independent predictors for OS identified in multivariate analysis included age and BM sCD52 level at response. Residual sCD52 at response may reflect residual disease, therefore correlating with shorter OS. We are currently evaluating sCD52 and sCD20 as prognostic factors for clinical outcomes in previously treated patients that received FCR as salvage therapy.
A Study of the Binding Mode and the In Vitro Activity of the Protein Tyrosine Kinase Inhibitor SKI-606 in the BCR-ABL Positive Cells.
Authors: Grafone Tiziana , Soverini Simona , Tasco Gianluca , Mancini Manuela , Boschelli Frank , Golas Jennifer , Frauling David , Colarossi Sabrina , Ottaviani Emanuela , Gnani Alessandra , Panagiota Giannoulia , Castagnetti Fausto , Casadio Rita , Rosti Gianantonio , Martinelli Giovanni , Baccarani Michele 
Published: October 2019

Abstract
Resistance to the BCR-ABL inhibitor imatinib mesylate (IM) is often caused by the selection of leukemic clones harboring mutations that destabilize the inactive conformation of BCR-ABL, to which IM preferentially binds, shifting the equilibrium toward the active kinase conformation. Hence the need for second -generation kinase inhibitors with a greater flexibility in binding to different BCR-ABL conformations. The 4-anilino-3 quinolinecarbonitrile SKI-606 is a novel Src and ABL kinase inhibitor. We report here that SKI-606 is a potent and antiproliferative agent when tested in K562 cell line and CD34+ cells from patients with chronic myeloid leukemia (CML) blast crisis. In K562 cells, SKI-606 treatment caused a dose-dependent decrease in cell viability accompanied by accumulation in subG1 phase, an effect not observed in BCR-ABL-negative HL-60 cells. Treatment of K562 with 100 nM SKI-606 for 24 hours caused a complete dephosphorylation of Lyn, Stat5 and Bcl-xl, while AKT and Bad phosphorylation was only diminished. Unexpectedly, the phosphorylation of BCR-ABL was less affected. SKI-606 treatment caused a shift to the subG1 phase also of CD34+ cells isolated from both IM-sensitive and resistant patients, the latter harboring the BCR-ABL mutations F359V, Y253H, E255V and E255K. The inhibitory concentration 50% (IC50) was 100 nM SKI-606 for Y253H, E255V, E255K and 1000nM for F359V. Cytofluorimetric analysis of cells from IM- sensitive CML patients indicated an accumulation in subG1 phase following treatment with SKI-606 alone or in combination with IM. Because the crystal structure of the BCR-ABL kinase domain in complex with SKI-606 has not yet been determined and the mode of binding of this inhibitor is unknown, we first used a molecular docking approach to determine SKI-606 binding mode to wild type (wt) form of the BCR-ABL kinase. We found that the interaction between SKI-606 and BCR-ABL was more stable when the activation loop was in the inactive conformation. Moreover, we found that SKI-606 retained the ability of efficiently binding all the above mentioned BCR-ABL variants, but not the T315I. Finally, we identified six BCR-ABL residues located around SKI-606 that, if mutated, could potentially be able to interfere with the SKI-606/BCR-ABL interaction: the charged residues K271, D381 and H361; the hydrophobic/aliphatic residues V299, A380 and M318.
These data help refining the use of SKI-606 for treatment of BCR-ABL positive leukemias.