bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Gene Expression Profiles in Acute Lymphoblastic Leukemia Cells That Discriminate Intracellular Thioguanine Nucleotide Accumulation in ALL Cells after In Vivo Treatment with Mercaptopurine.
Authors: Zaza Gianluigi , Cheok Meyling , Yang Wenjian , Deqing Pei , Cheng Cheng , Pui Ching-Hon , Relling Mary V. , Evans William E. 
Published: October 2019

Abstract
Thioguanine nucleotides (TGN) are considered the principal active metabolites exerting the antileukemic effects of mercaptopurine (MP). Numerous clinical studies have reported substantial inter-patient variability in intracellular TGN concentrations during continuation therapy of acute lymphoblastic leukemia (ALL). To identify genes whose expression is related to the intracellular accumulation of TGN in leukemia cells after in vivo treatment with MP alone (MP) or in combination with MTX (MP+MTX), we used oligonucleotide microarrays (Affymetrixâ HG-U95Av2) to analyze the expression of approximately 9,670 genes in bone marrow leukemic blasts obtained at diagnosis from 82 children with ALL. TGN levels were determined in bone marrow aspirates of these patients 20 hours after mercaptopurine infusion (1 g/m2 I.V). Because, as previously reported, patients treated with MP alone achieved higher levels of intracellular TGN compared to those treated with the combination, we used Spearman’s rank correlation to identify genes associated with TGN levels separately for the 33 patients treated with MP alone and the 49 with the combination (MP: median TGN: 2.46 pmol/5x106 cells, range: 0.01–19.98; and MTX+MP: median TGN: 0.55 pmol/5x106 cells, range: 0.005–3.31). Hierarchical clustering using these selected probe sets clearly separated the 33 patients treated with MP alone into two major groups according to TGN concentration (< 2.46 and > 2.46 pmol/5x106 cells; n=60 genes) and two major branches were also found for patients treated with the combination (< 0.55 and > 0.55 pmol/5x106 cells; n=75 genes). Interestingly, there was no overlap between the two sets of genes, indicating that different genes influence the accumulation of TGN when this drug is given alone or in combination with MTX. The association between gene expression profiles and TGN levels determined by leave-one-out cross-validation using support vector machine (SVM) based on Spearman correlation, was rho=0.60 (p<0.001) for MP alone and rho=0.65 (p<0.001) for MTX+MP, with false discovery rate (FDR) computed using Storey’s q-value (MP: 50% true positive, MTX+MP: 70% true positive respectively). Genes highly associated with the post-treatment TGN level in ALL patients treated with MP alone encode transporters, enzymes involved in the MP metabolic pathway and cell proliferation. Genes associated with post-treatment levels of TGN after combined therapy have been implicated in protein and ATP biosynthesis. Together, these in vivo data provide new insights into the basis of inter-patient differences in TGN accumulation in ALL cells, revealing significant differences between treatment with MP alone or in combination with MTX.
Progressively Intensified Chemotherapy: A Phase II Trial in Patients with Multiple Myeloma.
Authors: Farjami Sassan , Akhtar Adnan , Kancherla Rama Mohana , Liu Delong , Seiter Karen , Ahmed Tauseef 
Published: October 2019

Abstract
Background: A number of randomized and non-randomized studies have demonstrated the efficacy of the high-dose therapy with stem cell rescue. The efficacies of these treatment modalities were mainly related to the degree of myeloablation and destruction of the bone marrow microenvironment. We decided to evaluate the efficacy and toxicities of a progressively intensified chemotherapy followed by stem cell rescue in patients with multiple myeloma.
Methods: Between 1997 and 2000 twenty-eight patients (median age, 51years; range 38–70) consecutively enrolled in this study. Patients received VAD combination chemotherapy as induction regimen. Blood progenitor cells were collected following two cycles of cyclophosphamide, etoposide and granulocyte-colony stimulating factor (G-CSF). The chemotherapy intensified by giving melphalan at a dose of 140 mg/m2and mitoxantrone at a dose of 60 mg/m2 on day -7of 1st myeloablation followed by stem cell rescue on day 0. Between 56–94 days following 1st transplant patients received 2nd intensification by Melphalan at a dose of 200 mg/m2 on day -3 of 2nd myeloablation followed by stem cell rescue on day 0. After recovery from 2nd intensification patients received Interferon-alfa2b and prednison as maintenance therapy for 18 months.
Results: After induction there was 7%(2) complete response (CR), 72%(20) partial response and in 21%(6) their disease progressed (PD). Following escalation with cyclophosphamide and etoposide the CR rate was 21%(6), with 86%(24) overall response. After dose intensification with melphalan, mitoxantrone and 1st stem cell rescue the CR increased to 61%(17) with 89%(25) overall response. Following 2nd dose intensification with melphalan and stem cell rescue the CR increased to 68%(18) and overall response reached to 90%(24) Most non-hematologic toxicities were in the range of grade 0–2. Mucositis and diarrhea were the most severe toxicities associated with 1st and 2nd intensification. After median duration of follow up of 66.67 months the survival probability was 56.47% with 95 percent confidence interval of 42.65% and 70.29%.
Conclusion: Our study suggests that combination of cyclophosphamide with etoposide could induce remission in significant number of patients prior to aphresis and by decreasing tumor burden could reduce stem-cell contamination (in vivo purging). Also mitoxantrone in addition to melphalan as a standard preparative regimen could result in high rates of complete remission and overall response, which could be translated in to better overall survival.
Conditioning Regimens in Stem Cell Transplantations Facilitate Homing by Increasing Bone Marrow SDF-1 through Induction of SDF-1 Gene Transcription.
Authors: Zweegman Sonja , Janssen Jeroen J.W.M. , Kessler Floortje L. , Mus Adriana M.C. , van den Born Jacob , Huijgens Peter C. , Drager Angelika M. 
Published: October 2019

Abstract
Stromal Derived Factor-1 (SDF-1) is a key regulator of engraftment. The clinical relevance of SDF-1 is suggested by the relation between in vitro migratory capacity of CD34-positive cells towards SDF-1 and engraftment after stem cell transplantation (SCT). For better insight in engraftment after SCT clarifying the determinants of SDF-1 is therefore important. We investigated SDF-1 responses after chemotherapy and irradiation of the murine stromal M210B4 cell line and in allogeneic SCT patients. SDF-1 protein levels were measured in conditioned medium (CM) of the M210B4 cell line, in peripheral blood plasma and bone marrow plasma by ELISA. The migration supportive capacity of CM was tested by allowing CD34-positive cells to migrate over fibronectin coated transwells for 4 hours. Furthermore, sdf-1 gene expression was investigated by means of a quantitative PCR using mRNA from M210B4 cells or from buffy coats of peripheral blood and bone marrow cells.
Both irradiation and cytarabine treatment of M210B4 cells resulted in a significant ~2-fold increase in SDF-1 levels and a significant ~1.5-fold increase in migration of CD34-positive cells. Changes in protein levels correlated with those of mRNA: both treatments resulted in a significant ~2-fold increase in SDF mRNA copies.
In agreement with in vitro results, a significant ~3-fold increase in SDF-1 protein levels was induced by in vivo myeloablative and non-myeloablative conditioning regimens. The increase in SDF-1 was higher in BM plasma as compared to PB plasma, thereby significantly increasing BM-PB gradients (BM minus PB SDF-1 levels: 11.0±3.5 after versus 4.0±2.8 ng before conditioning). Corresponding with protein levels, sdf-1 mRNA increased in bone marrow cells of 4/5 patients (~40-fold increase, from 0.3±0.3% to 9.7±15.2% relative to GAPDH expression, n=4 of whom 2 received myeloablative and 2 non-myeloablative regimens). Wide ranges of increase in SDF-1 message (ranging from 0.26 to 104-fold increase) and protein levels (1.26 to 5.16-fold increase) were observed, which may be accounted for by differences in conditioning regimens.
We conclude that generation of an SDF-1 gradient over the blood-bone marrow barrier by conditioning regimens plays a role in engraftment. The introduction of reduced intensity stem cell transplantations challenged the idea that sublethal conditioning is a prerequisite for engraftment by preparing vacant niches. Our observation that both non-myeloablative and myeloablative regimens result in an increase in SDF-1 gradient, can be proposed as an explanation. Interestingly, the variation in increase of SDF-1 after different conditioning regimens indicate that homing efficiency may be improved by reconsidering the optimal moment of stem cell infusion and the agents used in conditioning regimens.
Immunological Recovery after Nonmyeloablative Transplant: A Prospective Study of 24 Patients Treated in a Single Center.
Authors: Bron Dominique , Hyunh Van , Dewilde Virginie , Bennani Jalil , Lewalle Philippe , Huynh Phuong , Leroy Rita , Crombez Patrick , Debusscher Louisette , Feremans Walter , Bernier Michel , Martiat Philippe 
Published: October 2019

Abstract
Background: Nonmyeloablative conditioning regimens are more and more widely used in the setting of stem cell transplant due to a reduced transplant related mortality. However, these conditioning regimens include more immunosuppressive agents and little data in terms of immunological recovery are found in the literature.
Population: 24 patients (pts) admitted for nonmyeloablative transplant from HLA identical donors were prospectively followed during a period of 1 year. All pts received a conditioning regimen consisting of rabbit ATG (fresenius), Fludarabine phosphate, Cyclophosphamide ( ARA-C for myeloid malignancies) cyclosporin A and mycophenolate mofetil (MMF). Lymphocytes markers expression as well as lymphocytes absolute numbers were studied to evaluate the cellular immunologic recovery. IgG, IgA and IgM levels were also monitored during one year. Pts were stratified according to the presence of GVHD(acute and chronic) or not.
Results: 24 pts with a median age of 52 (20–64) years old transplanted with an attenuated conditioning regimen, were evaluated. Median delay to recover 500 ANC and 20000 plt/ul was 8 days. Without GVHD, the pts recover a normal level of CD3, CD8, CD19,CD56 and CD45RO positive lymphocytes within 6 months. CD4+ and CD45RA + lymphocytes did not reach normal values within 1 year; Therefore the CD4/CD8 ratio remains low for more than 12 months. This observation explains the high incidence of oppotunistic infections in these pts even 6 months after transplantion. In our small seies,with or without GVHD neither IgA, nor IgM recovered within 1 year. IgG recovery is not evaluable because of human IVIG administration monthly after transplant.
Conclusion: our small series confirms the rapid hematologic recovery after nonmyeloablative transplant.Cellular immunological recovery without GVHD is achieved within 6 months for most of the lymphocytes subsets excepted the CD4+ lymphocytes who need more than 12 months to recover. IgM and IgA recovery is also very slow.
Haploidentical Allogeneic Versus Gene Modified Autologous Stem Cell Transplantation for Severe Combined Immunodeficiencies (S.C.I.D). The Risk/Benefit Balance Is in Favor of Gene Therapy.
Authors: Cavazzana-Calvo Marina , Hacein-Bey-Abina Salima , Saint-Basile Genevieve , Le Deist Françoise , Wulfraat Nicolas , Alexander Ian , Landais Paul , Blanche Stephane , Fischer Alain 
Published: October 2019

Abstract
For the last 35 years or so, allogeneic hematopoietic stem cell transplantation (HSCT) has been the only curative approach for patients affected by severe combined immunodeficiencies (SCID), a medical emergency. According to the most recent European survey haploidentical transplants allow a survival rate at 3 years of 75% (taking only into account patients transplanted since 1995). The mortality rate is heavily influenced by age at transplantation (being very low within young infants), in correlation with the infection burden and also the incidence of acute graft-versus-host reaction (GVHD). Between 1998 and 2003, 6 patients with NK(−) B(+) SCIDs (either gc or JAK3 deficiency) received an haploidentical HSCT at Necker Hospital, 3 of them died from an infection, one in the context of a severe GVHD. In addition, despite the improvement in the survival rate, over the time a number of long-term concerns have been detected including a frequent persistence of a B cell deficiency, and a decline in T-cell functions related to the absence of donor stem cell engraftment and may be also to a premature decline in the thymus function.
Therefore, several patients have received a second transplant with a low efficiency in an haploidentical setting.
These significant limitations set the rationale for the development of an alternative strategy such as gene therapy. From March 1999 up to May 2002, ten children with gc deficiency under the age of one year were enrolled.
All of them are alive today. The gc gene transfer into patients’ CD34(+) cells led in 9 out of 10 patients to the emergence of T and NK lymphocytes. It took 10 to 12 weeks to detect mature T cells in the periphery, a delay which is significantly faster than the one observed after haploidentical HSCT. In all but 2 patients, T cell counts normalized up to 5.3 years after gene therapy. The occurrence of two severe adverse events led to put transiently the trial on hold in order to understand the pathophysiology of these events and assess its overall risks. Following a thorough analysis of the retrospective data and a prospective analysis, it was concluded that the benefit/risk balance in favor of the gene therapy approach at least for patients older than 3 months, hence our gene therapy protocol has been reopened. An update of the clinical data will provided at the meeting.
t(3;14)(P14.1;Q32) Involving IGH and FOXP1 Is a Recurrent Chromosomal Aberration in MALT Lymphoma.
Authors: Streubel Berthold , Vinatzer Ursula , Lamprecht Andrea , Raderer Markus , Chott Andreas 
Published: October 2019

Abstract
Translocations t(11;18)(q21;q21), t(14;18)(q32;q21), and t(1;14)(p22;q32) are known to occur in MALT lymphoma. In a patient with MALT lymphoma of the thyroid a novel t(3;14)(p14.1;q32) was observed by cytogenetic analysis. Subsequent fluorescence in situ hybridization studies showed that the immunoglobulin heavy chain locus (IGH) was rearranged on chromosome 14. Long-distance inverse polymerase chain reaction identified FOXP1 as the partner gene on chromosome 3. Two FISH-assays were established to screen 90 MALT lymphomas, 8 splenic and 6 nodal marginal zone lymphomas for this aberration. Overall, 8 MALT lymphomas (9%) harbored t(3;14)(p14.1;q32); the aberration was detected in MALT lymphomas of the ocular adnexa (4 of 20), thyroid (2 of 5), and skin (2 of 20), but not in the stomach (n=20), salivary gland (n=20), and lung (n=5). Splenic and nodal marginal zone lymphomas were t(3;14)(p14.1;q32) negative. Further 38 MALT lymphomas with known t(11;18)(q21;q21), t(14;18)(q32;q21), or t(1;14)(p22;q32) did not reveal a t(3;14)(p14.1;q32). Most t(3;14)+ MALT lymphomas (7 of 8) harbored additional genetic abnormalities, such as +3. Real-time quantitative RT-PCR showed up-regulation of FOXP1 in cases with t(3;14)(p14.1;q32) or trisomy 3. This study identifies FOXP1 as a new translocation partner of IGH in MALT lymphomas.
Global DNA Methylation Profiling Demonstrates That Idiopathic Myelofibrosis Is Characterized by a Distinct Epigenetic Signature with Aberrant Methylation Changes in Genes Involved in Inflammation and Hematopoiesis
Authors: Opalinska J. , Sohal D. , Thompson R. , Zhou L. , Li Y. , Pahanish P. , Kotla V. , Kambhampati S. , Parmar S. , Friedman E. , Figueroa M. , Ye K. , Wickrema A. , Melnick A. , Greally J. , Pardanani A. , Verma A. 
Published: October 2019

Abstract
Chronic idiopathic myelofibrosis (MF) is a clonal hematopoietic disorder that leads to progressive marrow fibrosis and peripheral cytopenias. Very little is known about the role of aberrant DNA methylation in the pathobiology of this disease. Whole genome methylation was analyzed by a recently described novel method, the HELP assay (HpaII tiny fragment Enrichment by Ligation-mediated PCR; Khulan et al, Genome Res. 2006 Aug;16(8)) that uses differential methylation specific restriction digestion by HpaII and MspI followed by amplification, two color labeling and cohybridization to quantitatively determine individual promoter methylation. A whole genome human promoter array (Nimblegen) was used to determine the level of methylation of 25626 gene promoters by calculating HpaII/MspI cut fragment intensity ratio. Peripheral blood leucocytes from 9 patients with IMF were compared to 9 age-matched normal and anemic controls. Gene expression analysis was performed using 37K oligo maskless arrays using cDNA from the same samples. Methylation analysis showed that myelofibrosis samples clustered separately from normal and anemic controls when grouped by unsupervised clustering based on Pearson’s correlation coefficient. On the other hand, global gene expression demonstrated no clear cut differences between myelofibrosis and control samples suggesting that methylation profiling has greater discriminatory power when compared to conventional gene expression profiling. A high correlation (r=0.88–0.96) was observed between whole genome methylation profiles of matched sets of bone marrow and peripheral blood leucocyte samples from selected patients demonstrating that peripheral blood leucocytes can act as a valid surrogates for epigenomic analysis. Further analysis showed that genes aberrantly methylated in all myelofibrosis samples included v-myc, histone 2A, TNF, TNF Receptor1, FGF14 and others. Functional pathway analysis by Ingenuity showed that pathways involved in Inflammation and Cell signaling were the most affected by epigenetic silencing. Most interestingly, a large proportion of gene promoters were also aberrantly hypomethylated. These included genes for chemokine CXCL13, APC, IL-3, STAT2 and others. The pathways most activated by hypomethylation were involved in hematopoiesis and cell growth and proliferation demonstrating the biological validity of our analysis. Thus, our data demonstrates that myelofibrosis is characterized by distinct epigenetic aberrations that are preserved in peripheral blood leucocytes. These can be the basis of future studies on pathogenesis and diagnosis for this disease and lead to translational studies with agents targeting DNA methylation.
Dynamic Imaging of Fibrin Network Formation Correlated with Other Measures of Polymerization.
Authors: Weisel John W. , Chernysh Irina N. 
Published: October 2019

Abstract
The clotting time or gel point is commonly used in a variety of clinical assays, but little has been known about what it represents structurally because of the limitations of imaging technologies. The necessity of fixation and dehydration for electron microscopy means that only final clot structures, often distorted by preparation artifacts, can be observed, and there are severe limitations of image quality for conventional light microscopy. For similar reasons, we know almost nothing about the branching and lateral aggregation of fibrin that are essential for clot or thrombus stability. Turbidity, light scattering, or clot stiffness are useful to follow the time course of polymerization but reflect only overall clot properties. We visualized in real time fibrin network formation in the hydrated state, using deconvolution microscopy, which allows optical sectioning without the bleaching that accompanies confocal microscopy. Thus, the events during polymerization could be followed quantitatively over long periods of time. Videos will demonstrate the major observations. Individual mobile fibers were observed before the gel point. After gelation, an initial fibrin network, or scaffold, was seen, which evolved over time by addition of new fibers and elongation and branching of others. Furthermore, some fibers in the network moved chaotically for some time. A detailed, quantitative morphological analysis of network formation was carried out by superposition of images from different time points colorized to distinguish changes. We quantified network formation by the number of branch points, and longitudinal and lateral growth of fibers as a function of time. The distributions of fibers that reached a maximum of longitudinal growth and branch point formation both had maxima at the gel point but, surprisingly, some longitudinal growth continued and new branch points appeared after the gel point, requiring modification of existing models of fibrin polymerization. The cumulative percentage of fibers reaching their final length and the number of branch points attained maximum values at the time corresponding to that at which the turbidity reached approximately 60% of its maximum. Lateral growth reached a plateau at the same time as turbidity. Measurements of clot mechanical properties revealed that the clots achieved maximum stiffness and minimum plasticity well after branch point, as well as length changes and lateral growth of fibers, were completed. These results provide new information on the time sequence of events during fibrin network formation, which is important to understand both clotting and thrombosis and to allow modulation of clot properties.
Pilot Results: Pre-Treatment with Deferasirox Increases the Chances of Rapid Viral Response in Patients with Chronic Hepatitis C Infection Treated with PEG-Interferon/Ribavirin.
Authors: Goubran Hadi A. , Essmat Gamal , Morcos Hanaa H. , Amin Sherif N. 
Published: October 2019

Abstract
Chronic hepatitis C infection [CHCV] is a major cause of morbidity and mortality. It is treated with a combination of interferon and ribavirin [INF/RIBV] for 1 year in strain 1 & 4 prevalent in our geographic area 1. Iron overload is an important cofactor of disease outcome, enhancing inflammation, fibrosis and cirrhosis and predisposing to hepatocellular carcinoma. It also affects the response to conventional therapy2–3. We evaluated the impact of pre-treatment iron chelation using deferasirox on the outcome of combination therapy (160μg PEG-Interferon α-2-a (Reiferon-Retard) and ribavirin) in terms of early viral response defined as clearance or 2 log reduction in viral load at 12 weeks and rapid viral response defined as viral clearance by four weeks. The latter may imply a shortened duration of therapy to 6 months rather than a year, improving cost effectiveness and reducing side effects 4,5. The study included 30 patients with CHCV candidates for INF/RIBV therapy with a Metavir score of less than F3 by liver biopsy or fibrotest. The mean serum ferritin of patients prior to therapy was 520+/−98 ng/ml. Ten patients were subjected to iron chelation using deferasirox (15mg/Kg/day p.o.) for 6–8 weeks prior initiation of therapy (group I), bringing their serum ferritin to 309+/−74 ng/ml, whereas 20 patients started therapy without pre-treatment chelation (group II). Patients were followed up periodically both clinically and laboratory. HCV PCR both quantitative and qualitative were conducted at week 4 and 12. In 7 patients (70%) from group I, early viral clearance at 12 weeks, was reported compared to 12 (60%) in group II (p>0.05). Six patients out of the 7 cleared in group I and 6 patients out of the 12 in group II (p<0.01) had a rapid virologic response with complete viral clearance at 4 weeks. Pre-treatment with deferasirox may improve early viral response rates. It seems to favor rapid virologic response in CHCV patients treated with INF/RIBV with a potential shorter duration of therapy, significant cost reduction and less side effects. Larger studies are needed to confirm the results of this pilot work.