bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Bioinformatic Approach to CLL IGHV Sequence Analysis Identifies Extensive Ig Sequence Archetypes among BothMutated and Unmutated Sequences.
Authors: Messmer Bradley T. , Raphael Benjamin J. , Aerni Sarah J. , Widhopf George F. , Rassenti Laura Z. , Toy Traci L. , Kipps Thomas J. 
Published: April 2020

Abstract
Several recent studies have pointed towards a number of sets of CLL patients with highly similar IgV genes, both in terms of V, D, J segment and light chain use and also heavy chain third complementarity determining region (CDR3) architecture and amino acid composition. These findings support the notion that antigen may drive development or perpetuation of the leukemic cells. To effectively mine the available Ig sequence databases, we developed a novel sequence similarity and clustering algorithm that incorporates the mechanistic knowledge of IgV gene recombination. CDR3 sequences were initially aligned using the conventional blosum62 based scoring matrix, then rescored based on the junctional annotations. In this way, the method gives greater weight to sequence similarity created as a consequence of the VDJ recombination process, rather than simple germline homology. This modified scoring matrix allows the creation of more robust sequence “clusters” and is not restricted to sequences composed of the same germline genes. Preliminary analysis with this method on a collection of more than 1000 CLL IgV gene sequences has identified over 40 clusters, including all that have been previously described. Interestingly, a species abundance estimator indicates additional clusters of IgV genes in CLL remain to be discovered. Additionally, we performed a focused evaluation of over 100 VH4-34 containing sequences expressed by CLL cells of unrelated patients. The VH4-34 gene is among the most commonly used IVH genes expressed in CLL, has a curious bi-phasic distribution of mutational frequencies among different CLL cases, and can encode antibodies with specificity for the linear polylactosamine carbohydrate antigen “i” found on neonatal red blood cells. Prior studies by the Chiorazzi group identified a subgroup of patients with CLL cells that expressed remarkably similar mutated VH4-34 genes encoding isotype-switched Ig. Using the method described above, seven additional clusters of CLL cases that expressed highly related VH4-34-encoded Ig were identified, including three clusters containing sequences with a mutated VH4-34. The mutations seen within these clusters have a spectra that is distinct from other VH4-34 sequences from CLL, normal plasma cells, or marginal zone B cells. Furthermore, within each cluster there were conserved replacement mutations not commonly found in the other VH4-34 sequences. This clearly indicates specific selective pressures subsequent to IgV gene rearrangement and implies that the expressed Ig were selected for binding to several distinct antigens or epitopes. However, redundant antigen specificities encoded by different sequence clusters can not be excluded and the number of driving antigens may still be quite restricted. Comparative analysis of normal sequence collections is ongoing.
Thrombotic Microangiopathy™ after Allogeneic Peripheral Blood Stem Cell Transplantation with Nonmyeloablative Conditioning (NMSCT) Compared with Myeloablative Conditioning (MSCT).
Authors: Willems Evelyne , Baron Frédéric , Fillet Georges , Beguin Yves 
Published: April 2020

Abstract
Background: Thrombotic microangiopathy (TM) is a severe complication of allogeneic transplantation. The use of CsA for GvHD prophylaxis and unrelated donor appear to be the most significant risk factors for TM after transplantation with conventional myeloablative conditioning (MSCT). Allogeneic transplantation with reduced-intensity conditioning (RIC) is associated with a similar risk of TM, but TM has never been studied after NMSCT.
Purpose: To determine the risk factors, incidence and outcome of TM in NMSCT compared to MSCT.
Patients: Consecutive patients undergoing NMSCT (group 1, n=103) or MSCT (group 2, n=136) in our center between 1995 and 2004 were retrospectively analysed for TM. Median age was 55 vs 34 yrs in groups 1 and 2 respectively (p&lt;0.0001). Donor was unrelated for 52% of the patients in group 1 and for 38% in group 2 (p=0.0287).
Results: TM was diagnosed in 18 (20%) and in 30 (26%) patients in groups 1 and 2, respectively (NS). Most cases were grade 2 TM (18/18 in group 1 and 24/30 in group 1, NS). Neurological signs were present in 50% of the patients in group 1 and 57% in group 2 (NS). In both groups, TM was significantly associated with unrelated donor (p=0.0476 in group 1, p=0.0005 in group 2) and with CMV disease (p=0.0332 in group 1, p=0.0346 in group 2) but not CMV infection. AGvHD of all grades was correlated with TM in group 1 (p=0.0004) but only severe (grade 3–4) AGvHD in group 2 (p&lt;0.0001). Median time of onset of TM was 39 (range 18–157) days in group 1 and 38 (range 0–428) in group 2. First line treatment consisted in switching GvHD prophylaxis to alternative treatment (including tacrolimus) in 54% of the patients and plasmaphereses (36±10 in group 1 and 21±4 in group 2) in 63%. Vincristine (in 11% and 13% of the patients in groups 1 and 2, respectively) and other treatments were rarely used. Forty-four % of the patients died without achieving resolution of their TM in group 1, and 50% in group 2 (NS). For patients who responded to therapy, median duration of TM was 57 (range 5–165) days in group 1 and 46 (range 5–163) days in group 2 (NS). In group 1, the 100-d and 1-yr survival rates were 64% and 28% for patients who developed TM, and 84% and 69% for those without TM, respectively (p=0.0002). In group 2, survival was also significantly reduced in the case of TM (48% vs 70% at day 100 and 23% vs 53% at 1 yr, respectively, p=0.0126).
Conclusion: TM remains a frequent and severe complication of allografting. Its incidence and severity in NMSCT is not decreased compared to MSCT and the same factors appear to contribute to its development.
Risk Factor Analysis for Thrombotic Microangiopathy after Reduced Intensity or Myeloablative Allogeneic Hematopoietic Stem Cell Transplantation.
Authors: Nakamae Hirohisa , Yamane Takahisa , Kiyoyuki Hagihara , Takeoka Yasunobu , Sakamoto Erina , Nakane Takahiko , Nakamae Mika , Koh Ki-Ryang , Ohta Kensuke , Hino Masayuki 
Published: April 2020

Abstract
Thrombotic microangiopathy (TMA) impairs long-term survival after allogeneic hematopoietic stem cell transplantation (HSCT). As the allogeneic HSCT procedure has developed, addressing risk factors for TMA has become more complicating. The aim of this study was to investigate the impact of transplant-associated factors on TMA incidence of in patients who underwent HSCT in various settings. One hundred and twenty-three consecutive allogeneic HSCT patients (15 to 69 years old) with hematologic diseases receiving myeloablative and reduced intensity conditioning were evaluated retrospectively. Of 123 HSCTs, 22 (17.9%) patients were diagnosed with TMA after HSCT. The median time to the diagnosis of TMA from HSCT was 33.5 days (range, 1–126). In 21of 22 patients, TMA occurred within 120 days after HSCT. Ten of 22 patients with TMA received some treatments for TMA. Any treatment for TMA including plasma exchange, tapering immunosuppressive agents, avoiding platelet transfusion, and administration with fresh frozen plasma and/or anti-thrombin III preparation, did not significantly improve overall survival in patients with TMA compared with those not treated for TMA. Using univariate Cox proportional hazard model analysis, age, HLA mismatch, GVHD grade II–IV, the use of FK506 for GVHD prophylaxis and the use of high-dose Bu were significantly associated with an increased incidence of TMA after HSCT. Furthermore, multivariate analysis showed the significance of GVHD grade II–IV, the use of FK506 and the use of high-dose Bu (16 mg/kg) persisted. On the other hand, the use of half-dose Bu (8 mg/kg) for conditioning was not significantly associated with increased TMA. The hazard ratios of the use of FK506, the use of high-dose Bu (16 mg/kg) and GVHD grade II–IV for TMA were 8.7 (95% CI 2.0–37), 5.7 (95% CI 1.5–21) and 3.4 (95% CI 1.3–9.1), respectively. In the present study, reduced intensity conditioning did not have an advantage over myeloablative conditioning for decreasing the incidence of TMA after HSCT. Our results also showed that high-dose Bu (16 mg/kg) for a conditioning and FK506 for a prophylaxis of GVHD might contributes more to TMA onset after HSCT than other agents.
First Molecular Characterization of a Family with Combined FV and FVII Deficiency.
Authors: Traynis Ilana , Jones Carol D. , Gibb Connie B. , Acharya Suchitra , Zehnder James L. 
Published: April 2020

Abstract
Combined factor V and VII deficiency is a rare bleeding disorder, with 3 cases reported in the literature. None of these cases were characterized at a molecular level. We now report a 4th case of factor V and VII deficiency, and for the first time characterize the factor V and VII mutations/polymorphisms in the proband and parents.
Case history: The proband is a 5-year-old female who presented with microscopic hematuria and mild mucosal bleeding. She has 47% FV activity and 38% FVII plasma activity. Her father has a history of delayed wound healing and mild mucosal bleeding and her mother has history of mild epistaxis, menorrhagia and gingival bleeding.
Results: The proband was heterozygous for a novel FV mutation, a one base deletion in exon 4 (524delG) introducing a frameshift and resulting in premature truncation of translation 33 amino acids later. In addition, she was heterozygous for 4 previously described factor VII polymorphisms: a 10-bp insertion [CCTATATCCT] at -323 in the 5′ region of the promoter, a G to A substitution in intron 1a (73 g&gt;a), and the R353Q polymorphism in exon 8 of the F7 gene. These 3 polymorphisms have been found to be in strong allelic association in the Italian population, with mild FVII deficiency (Peyvandi et al, 1999). In addition, a R315W mutation was found in exon 8. This mutation has been reported to decrease both FVII coagulant function and factor X activation (Furlan Freguia et al, 2004). The mother was also heterozygous for FV and FVII deficiency, with FV 524 delG and FVII R315W, while as expected the father was heterozygous for the factor VII allele with the 3 associated FVII polymorphisms (Table 1). Thus the proband is heterozygous for FV deficiency and a compound heterozygote for Factor VII deficiency, inheriting FVII mutations from both parents. This is the first molecular characterization of a family with combined factor V and VII deficiency, and also the first family described with 2 different forms of combined FV and FVII deficiency within the same family. These results are consistent with this syndrome being due to chance co-inheritance of FV and FVII mutations rather than a post-translational defect as seen in combined FV and FVIII deficiency.
Table 1 F5 524delG F7 R315W F7 -323 F7 IVS1 73 g&gt;a F7 R353Q Summary of mutations/polymorphisms in a family with combined factor V and factor VII deficiency. X denotes presence of a given mutation/polymorphism in an individual. Proband X X X X X Mother X X Father X X X
Genetic and Phenotypic Analysis of Families with Inherited Hypo- and Dys-Fibrinogenemia. Fibrinogen Bratislava.
Authors: Batorova Angelika , Horvathova Daniela , Mistrik Martin , de Moerloose Philippe , Neerman-Arbez Marguerite 
Published: April 2020

Abstract
Inherited hypofibrinogenemia (hypo-FBG) and dysfibrinogenemia (dys-FBG) are rare blood coagulation disorders caused by quantitative or qualitative defects of fibrinogen. We reviewed the clinical course in 47 individuals with dys-FBG and 16 patients with hypo-FBG with median fibrinogen coagulant/antigen levels of 0.76/2.8 and 1.1/1.2 g/L, respectively. Genetic analysis was performed in 5 families (16 individuals) with dys-FBG and 4 families (8 individuals) with hypo-FBG.
In the dysfibrinogenemia group 21 (45%) individuals were asymptomatic, 24(51%) patients suffered from bleeding and/or prolonged wound healing (only four had serious bleeding) and 2(4%) patients had a history of thrombosis. A total of 96 surgeries were performed without preoperative fibrinogen replacement in 31 dys-FBG patients, only 9 (9%) procedures were complicated with bleeding, two requiring fibrinogen substitution. Genetic analysis in dysfibrinogenemia has revealed heterozygous mutation in FGA exon 2 (Aα Arg16 His) known to cause delayed fibrinopeptide A cleavage by thrombin in 6 individuals (3 families). Five patients from two other families were heterozygous for a novel mutation in FGA exon 2 (Aα Gly13Glu). Fibrinogen coag/Ag median levels were comparable for both mutant genotypes: 0.5/2.9 g/L and 0.56/2.8 g/L, respectively.
In the hypofibrinogenemia group 6/14 (43%) patients had mild spontaneous bleeding, 8/36 (22%) surgeries performed in 12 patients w/o replacement were complicated with bleeding. A novel mutation in FGG exon 1 (Trp3 Stop) was identified in heterozygosity for 3 patients (3 families) with FBG coag/Ag median level of 1.1/1.2 g/L. An additional unrelated patient with a fibrinogen level of 0.7 g/L and serious postpartum bleeding was heterozygous for a novel mutation in FGG exon 7 (Trp253Cys) - Fibrinogen Bratislava.
Micro-Array and Protein Analyses Reveal a Preferential Autocrine VEGF Survival Loop in CD38+ Sub-Clones When Compared with CD38− Sub-Clones Derived from the Same CLL Patient.
Authors: Pepper Chris , Ward Rachel , Starczynski Jane , Rowntree Clare , Pratt Guy , Mills Ken , Fegan Chris 
Published: April 2020

Abstract
CD38 expression is a marker of poor prognosis in chronic lymphocytic leukemia (CLL) but to-date no clear rationale for this has been elucidated. Using high speed cell sorting and subsequent gene expression profiling, we investigated the transcriptional characteristics of purified CD38+ and CD38− sub-clones derived from the same patient (n = 12). Our analysis revealed a distinct, differential gene expression profile between CD38+ and CD38− subsets with 35 genes found to be consistently over expressed in the CD38+ cells (of which CD38 was one; 9.1 fold). Of particular interest were four genes, CXCL-2 (9.4 fold), vascular endothelial growth factor (VEGF) (5.8 fold), MIP1α /CCL3 (5.4 fold) and Interleukin 1β (IL-1β ) (4.1 fold). In a number of different tumor models IL-1β has been shown to induce the expression of CXCL-2, VEGF, and MIP1α resulting in angiogenesis, survival signaling and/or tumor proliferation. Protein analysis revealed 2–3 fold elevated levels of IL-1β and VEGF in CD38+ cells confirming that the elevated transcription was translated. Furthermore, the differential transcription of these genes corroborates our previous findings; CD38+ cells have a higher proliferative index and higher levels of the anti-apoptotic protein Mcl-1. Our data strongly suggests that the CD38+ clones preferentially utilise an autocrine VEGF loop and given that the CD38− clones also express VEGF receptor the potential for bystander paracrine effects of secreted VEGF seem likely in bimodal patients. Therefore, the relative over expression of IL-1β and VEGF provide a rationale for the disease progression and poor clinical prognosis of CD38+ CLL patients.
A Randomized, Double Blind Trial, of Hydroxychloroquine for the Prevention of Graft-Versus-Host Disease after Allogeneic Peripheral Blood Stem Cell Transplantation.
Authors: Fong Tom , Trinkaus Kim , Adkins Douglas R. , Vij Ravi , Devine Steven , Tomasson Michael , Goodnough Lawrence T. , Graubert Timothy , Shenoy Shalini , DiPersio John F. , Khoury Hanna J. 
Published: April 2020

Abstract
Hydroxychloroquine (HCQ) is an immunosuppressive lysosomotropic amine that has activity against graft-versus-host disease (GVHD). We previously reported low incidences of acute GVHD in unrelated donor transplant recipients who received prophylactic HCQ in addition to standard GVHD prophylaxis (BBMT2003; 9: 714–721). We herein report results of a single-institution phase III trial, in which 95 recipients of matched sibling allogeneic peripheral blood stem cell transplantation were randomized to receive, in a double-blind fashion, and in addition to prophylactic cyclosporine A (CSA), HCQ or placebo starting 21 days pre-transplant and continued until d+365. HCQ was very well tolerated and not associated with side effects. The addition of HCQ had no effects on lymphocyte subsets both pre- and post-transplant. Overall, the incidence of acute GVHD was 59% in both arms, and severe acute GVHD occurred in 11% (HCQ) and 14% (placebo) (p=0.76). Sixty-one and 46% of patients developed chronic GVHD in the placebo and the HCQ arms, respectively (p = 0.15). With a median follow-up of 18 months, relapse-free and overall survivals were comparable in both groups. In summary, in this randomized trial, the addition of HCQ to single agent CSA was not associated with a reduction of either acute or chronic GVHD; additionally, no significant effects on relapses or survival were observed.
Clinical Outcomes and the Impact of Anti-Thymocyte Globulin (ATG) and Chronic Graft Versus Host Disease (cGVHD) Following Pediatric Allogeneic Stem Cell Transplantation: A Comparison between Peripheral Blood and Bone Marrow as a Source of Stem Cells.
Authors: Cheema Parneet , Desai Sunil , Anderson Ronald , Coppes Max , Lewis Victor A. 
Published: April 2020

Abstract
INTRODUCTION: The use of peripheral blood as a source of stem cells for pediatric allogeneic stem cell transplantation remains controversial. We present a retrospective analysis evaluating the safety and efficacy of allogeneic peripheral blood stem cell transplantation (PBSCT) compared to allogeneic bone marrow transplantation (BMT) for the treatment of acute leukemia at our centre. The impact of ATG added to the treatment regimen was also evaluated in this analysis.
METHODS: A chart review was conducted on all pediatric patients who underwent an allogeneic stem cell transplant for acute leukemia between April 1991 and August 2003 at the Alberta Children’s Hospital. All patients who received stem cells from HLA matched or one-antigen mismatched donors were included in this analysis. Data were analyzed using SPSS.
RESULTS: 85 children (ages 9 months to 17 years) met study criteria. 24 patients underwent a PBSCT while 61 patients, a BMT for the treatment of either ALL (n=54) or AML/MDS (n=31). Median follow up time was 5.9 years. Six of 24 patients in the PBSCT group, and 30 of the 61 patients in the BMT group received ATG (p=.042). There was a trend towards increased overall survival (OS) at 5 years following PBSCT (p=.078). Disease free survival (DFS) at 5 years following PBSCT and BMT was similar (p=.297). Subgroup analysis found no difference in OS or DFS between PBSCT and BMT in patients receiving (p=.221, p=.820) or not receiving ATG as part of the conditioning regimen (p=.448, p=.820). Chronic GVHD was increased following PBSCT (45.8%) compared to BMT (19.7%) (p=.015). The rate of severe cGVHD, however, was not significantly different (25% vs. 11.5% for PBSCT and BMT, p=.119) between the two groups. No patients receiving ATG prior to PBSCT developed cGVHD (p=.009). Addition of ATG to the transplant regimen had no impact on the rate of cGVHD following BMT (p=.221). There was no increase in mortality due to cGVHD following PBSCT (p=.243) or BMT (p=.865). Although, there was a trend to improved DFS in patients who developed cGVHD following PBSCT, this was not statistically significant (p=.057). Despite a statistically significant increase in TRM found in all patients with cGVHD at one year post-transplantation (p=.048), there was no difference in TRM between the PBSCT (4.2%) and BMT (14.8%) groups (p=.173).
CONCLUSION: Allogeneic PBSCT is a safe and effective alternative to allogeneic BMT for the treatment of acute leukemia in the pediatric population. Although there is an increased rate of cGVHD following PBSCT this does not appear to influence OS, DFS or TRM in our analysis. Addition of ATG into the transplant regimen decreases the occurrence of cGVHD after PBSCT. Studies to further assess the role of ATG in PBSCT are warranted.
Chronic Cutaneous GVHD Does Not Correlate with Frequency and FoxP3 Gene Expression of Regulatory T Cells.
Authors: Haeusermann Peter , Tabellini Laura , Flowers Mary E. , Martin Paul J. , Carpenter Paul A. , Hansen John A. 
Published: April 2020

Abstract
OBJECTIVE: The pathogenesis of chronic GVHD and particularly of its skin involvement is incompletely understood. Regulatory CD4+CD25+ T-cells have been shown to influence acute and chronic GVHD disease and so far heterogeneous results considering the frequency of these cells in chronic GVHD have been published. Additionally, reports indicate that chronic GVHD is associated with reduced expression of FoxP3 of these specific T-cells potentially related to posttransplant thymic insufficiency. These investigations have so far not been conducted in the particular setting of isolated chronic cutaneous GVHD. Our objective therefore was to investigate number, immunophenotype and gene expression of T-cells and particularly of regulatory T-cells in whole blood, CD4-enriched T-cells and regulatory T-cells in these patients. Moreover, as immunosuppressive drugs (calcineurin inhibitors and Rapamycine) have been shown to influence the frequency of regulatory T-cells in vitro, our focus was to specifically study highly selected patients without immunosuppressive medications including cyclosporine, FK-506, Rapamycine, Glucocorticosteroids and MTX and with or without active chronic cutaneous GVHD.
METHODS: Since June 2005, 14 patients more than 365 days posttransplant because of hematologic malignancy and 4 normal controls have been investigated in this still ongoing study clinically and by T-cell immunophenotyping (whole blood, CD4+ T cells and regulatory T-cells) and gene expression (FoxP3, Il–10 and TGF-beta) with real time PCR.
RESULTS: Of all patients included so far, preliminary results indicate, that patients without GVHD at all and without immunosuppressive drugs as well as patients with isolated chronic cutaneous GVHD and off immunosuppressive drugs have a comparable amount of regulatory T-cells and level of gene expression for FoxP3. Patients within these two highly selected subgroups do not have clinical and/or laboratory evidence for gastrointestinal or liver affection.
CONCLUSION: With respect to our preliminary results, active chronic cutaneous GVHD in posttransplant patients after day 365 is not related to a decreased number of regulatory T-cells as well as to a reduced level of FoxP3 expression.