bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal Structure of the C2 Domain of Lactadherin and Computational Docking of Phosphatidyl-L-Serine.
Authors: Shao Chenghua , Head James F. , Seaton Barbara A. , Gilbert Gary E. 
Published: October 2019

Abstract
Lactadherin is a phosphatidyl-L-serine (Ptd-L-Ser)-binding protein that decorates the membranes of milk fat globules. Lactadherin is also secreted by macrophages, engaging Ptd-L-Ser on the membranes of apoptotic cells and hastening clearance by the macrophages. Sequence homology between the lectin-like C1 and C2 domains of lactadherin and those of factor VIII and factor V correlates with the capacity of lactadherin to compete for sites on Ptd-L-Ser-containing membranes and function as a potent anticoagulant. The C2 domain of lactadherin contains a major Ptd-L-Ser binding motif. Solution studies have shown that binding of the phospho-L-serine head group exhibits stereospecificity, consistent with the existence of one or more specific binding sites on the protein. Neither the three-dimensional structure of the lactadherin C2 domain nor the identity of specific residues that interact with Ptd-L-Ser have been determined. We have solved the crystal structure of the bovine lactadherin C2 domain (Lact-C2) at 1.67 Å resolution. The β-barrel protein core, composed of eight anti-parallel strands, is homologous with the previously published structures of the factor VIII C2 domain (fVIII-C2) and factor V C2 domain (fV-C2). The loops on the lower surface of Lact-C2 display four water-exposed hydrophobic amino acids, reminiscent of the membrane-interacting residues of fVIII-C2 and fV-C2. These hydrophobic amino acids, Trp26, Leu28, Phe31, and Phe81, form a diamond-shaped hydrophobic patch on the lower surface of Lact-C2. This hydrophobic patch is well positioned to interact extensively with the phospholipid membrane. The longest loop, predicted to participate in membrane binding, has a W-like shape that contrasts with the simpler shapes adopted by the corresponding loops of fV-C2 and fVIII-C2. Furthermore, in Lact-C2 glycine residues within putative membrane-interacting loops appear likely to provide conformational flexibility that may facilitate Lact-C2 binding to the membrane. To investigate potential Ptd-L-Ser binding sites on the protein, computational docking studies were performed, utilizing the program AutoDock. A Ptd-L-Ser analog with acetyl moieties replacing both acyl chains was utilized as the docking ligand. This approach avoided spurious identification of non-specific binding sites for acyl chains, which would naturally be immersed in a membrane bilayer. We identified two candidate Ptd-L-Ser binding sites that could engage the hydrophilic head group of Ptd-L-Ser in a stereoselective manner. The binding pocket for the better of the two solutions is not homologous with the Ptd-L-Ser binding sites previously proposed for fVIII-C2 or fV-C2. These results provide the basis for a testable hypothesis rationalizing the efficient phospholipid binding of lactadherin vs. factor VIII and factor V and the mechanism for Ptd-L-Ser stereoselectivity.
The Feasibility of Combining Daunorubicin, Clofarabine and Gemtuzumab Ozogamicin Is Feasible and Effective. A Pilot Study.
Authors: Burnett Alan K. , Kell William J. , Hills Robert K. , Russell Nigel H. , Yin John , Hunter Ann , Culligan Dominic 
Published: October 2019

Abstract
New treatment combinations are required for older patients with AML. Clofarabine is a novel nucleoside analogue which has been shown in several phase 2 studies in older patients to be active alone or in combination. Gemtuzumab Ozogamicin (GO) is also active in older patients and is currently undergoing evaluation in several randomised trials. As part of the proposed UK NCRI AML16 Trial for patients over 60 years we have undertaken a Pilot Trial to establish the feasibility combining standard dose Daunorubicin (D) (50mg/m2 days 1,3,5), Clofarabine (Clo) and GO (3mg/m2) as a novel combination, with the intention to compare D+Clo vs D+Ara-C both +/− GO on day 1. Five treatment cohorts were planned. Daunorubicin at a dose of 50mg/m2 is included in all cohorts. Cohorts 1–4 combine D with Clo at a dose level of 15mg/m2, 20mg/m2, 25mg/m2 and 30mg/m2 given on days 1–5 for 2 courses, to establish the feasible Clo dose in combination. Cohort 5 comprises D + feasible Clo dose given as above + GO 3mg/m2 on day 1 of course 1. Each cohort initially comprised 6 patients, and cohorts were expanded based on toxicity scoring. If toxicity criteria were satisfied the next cohort was opened. Thirty-four patients have been recruited. Of 6 patients in cohort 1 (15mg) 5 achieved CR without toxicity with one having refractory disease; of 7 patients in cohort 2 (20mg) 6 achieved CR with 1 having refractory disease; of 10 patients in cohort 3 (25mg) 4 achieved CR, 3 had refractory disease and 3 had induction deaths; and of 9 patients in cohort 4 (30mg) 5 entered CR, 2 had RD and 2 ID. Based on this, a dose of 20mg/m2 was chosen for clofarabine. So far cohort 5 has recruited 2 patients, both of whom have entered CR. This cohort will shortly be completed.
Toxicity: No toxicity of grade >2 in AST and ALT was seen in any cohort; one patient on Clo (30mg) had a transient grade 3 bilirubin elevation after courses 1 and 2. One patient (30mg) had grade 4 renal toxicity. The mean time on antibiotics was 13.1 days with no difference between the cohorts. The median time to recovery of ANC was 19 (17–24) days and platelets 19 (14–21) days.
Conclusion: The combination of Daunorubicin 50mg/m2 on days1, 3 and 5 and Clofarabine 20mg/m2 days 1–5 with Gemtuzumab Ozogamicin 3mg/m2 on day 1 is an effective and feasible combination for prospective evaluation.
A Multicenter Randomized Comparison of Maintenance Treatment with Androgens in Elderly Acute Myeloid Leukemia after ICL Regimen as Induction Therapy: Results of the Goelams-2002 Study.
Authors: Pigneux Arnaud , Himberlin Chantal , Hunault-Berger Mathilde , Witz Francis , Recher Christian , Harousseau Jean-Luc , Tournilhac Olivier , Berthou Chistian , Escoffre-Barbe Martine , Guyotat Denis , Fegueux Nathalie , Delain Martine , Lioure Bruno , Bauduer Frédéric , Jourdan Eric , Bouscary Didier , Legros Laurence , Perry Frédéric , Milpied Noel-Jean , Bene Marie-Christine , Ifrah Norbert , Sotto Jean-Jacques 
Published: October 2019

Abstract
In an attempt to improve the outcome of acute myeloid leukemia in older patients, we performed a multicenter randomized trial evaluating the possible benefit of androgens during post remission therapy. All patients received the ICL regimen as induction (Idarubicin, 8mg/m2 d1–5; Cytarabine, 100mg/m2 d1–7 and Lomustine, 200mg/m2 d1). All patients were randomized at the time of diagnosis to receive, after achieving CR or PR, a maintenance therapy including or not androgens. Maintenance therapy consisted of 6 courses of reinduction with idarubicin (8mg/m2 d1) and cytarabine (100mg/m2d1–5, subcutaneously) every 3 months, and, between these courses, a continuous regimen of methotrexate and 6-mercaptopurine. Patients randomized with androgens additionally received 10 to 20 mg according to body weigh of norethandrolone daily from CR/PR on, for up to 2 years. Between June 2002 and January 2005, 330 patients aged ≥ 60 years (median 70 yrs, range 60–86) were included. CR, PR, failure and death rates after induction were 69 %, 6%, 9% and 15% respectively. The median follow-up for the 330 patients was 26 months.
Among the 249 patients who achieved remission, 119 had been randomized with norethandrolone and 130 without. The 2 arms were balanced according to age, sex-ratio, performance status, FAB, WBC as well as platelets counts, peripheral blood and bone marrow blasts counts and cytogenetic groups (low risk: t(8;21), inv(16); high risk: del(5), del(7), del(11q), complex karyotype; standard-risk: normal karyotype and other aberrations). Differences in CR rates were only related to the latter parameter of cytogenetic features (P = 0.005).
For the whole cohort of patients DFS at 3-years was 23±3% (median 13 months) and OS at 3 years was 29±3% (median 15 months). For patients who achieved CR or PR and had been randomized, the addition of androgens did not influence either DFS (P = 0.6) or OS (P = 0. 9), even when considering age groups, high/low WBC, or cytogenetic features.
In conclusion, the ICL regimen followed by six reinductions and two years maintenance therapy induce high CR rates and improve OS and DFS. However the addition of androgens did not decrease the relapse rate.
Induction Therapy with Fludarabine, ara-C and G-CSF Results in Improved Event Free Survival in Core Binding Factor Leukemia.
Authors: Borthakur Gautam , Kantarjian Hagop , Wang Xuemei , Giles Francis , Cortes Jorge E. , Pierce Sherry , Estey Elihu H. 
Published: October 2019

Abstract
Previously (Blood2001;98:3575–3583) we reported that pts with inv (16) or t(8;21) (CBF) seemed to benefit from receiving fludarabine + ara-C (FA) rather than idarubicin + ara-C (IA), although other groups did not. Ara-C doses were 2g/m2 daily X 4–5 with FA and 1.5g/m2 daily X 2–4 by continuous infusion with IA. Because this observation was based on only 14 CBF pts given FA we proceeded, from 2000-present, to give all CBF pts FA either with (2000–2002; 22 pts) or without G-CSF (2003-present; 45 pts) on the days when FA was administered. Idarubicin(12 mg/m2 daily X 3) was given only if pts presented with WBC > 50,000, forcing start of treatment before cytogenetic results were known; once CR was achieved and CBF status was known, pts received 6 courses of post-remission therapy with FA (or FA +GCSF, FLAG) as described above. Median age was 41.5 years (range 16–83), 61 were male, 16 patients had antecedent hematologic disorder (AHD), 96 patients had ECOG performance status (PS) ≤ 1. One hundred and six patients (93%) achieved complete remission (CR). Events were defined as death, failure or relapse. Median time to event was 91 weeks and estimated EFS at 10 years was approximately 40%. Event-free survival (EFS) was compared in the 67 pts treated with FA or FLAG with EFS in 47 pts treated with IA +/− GCSF (IA/IAG). Because IA/IAG was given to CBF pts from 1991–2000 and FA or FLAG from 2000-present, we compared covariate-adjusted EFS in 436 pts with cytogenetics other than CBF according to whether they received IA before or after 2000 to estimate “period-effect”.EFS was superior in the earlier period, and this difference, seeming to inherently favor IA/IAG rather than FA or FLAG, was accounted for in the comparisons of these treatments in the CBF group. Preliminary analyses suggested that EFS in CBF pts was similar between IA and IAG (these groups were considered together for subsequent analyses) and longer with FLAG than with FA or IA/IAG (p= 0.06). After adjustments for covariates (age, WBC,platelets, marrow blasts etc) we compared EFS with FA, FLAG ,and IA/IAG, using both standard (Cox regression) and Bayesian approaches. The Bayesian model indicated that the posterior probability that FLAG was superior to IA/IAG was 0.98, and that, among pts given FA, the posterior probability that FLAG was superior to FA was 0.91. The Cox model indicated that the risk of an event with FLAG relative to IA/IAG was 0.84 (p = 0.07). A possible explanation for the seeming superiority of FLAG is the ability of G to increase accumulation of fludarabine-triphosphate in blasts during therapy (Clin Cancer Res1995; 1:169–178).
Figure Figure Figure Figure
Generation of Acute Myeloid Leukemia (AML)-Specific Autologous CD4 and CD8 T Cell Lines by Limiting Dilution AML Dendritic Cell Culture.
Authors: Zhong Rui-kun , Lane Thomas A. , Ball Edward D. 
Published: October 2019

Naturally occurring cytotoxic T cells directed against various leukemia associated antigens (LAA) expressed by acute myeloid leukemia (AML) cells have been described. However, these LAA-specific T cells are rare and obviously unable to initiate effective anti-leukemia responses. The challenge is how to investigate, select, activate and expand the rare LAA-specific T cells from the vast population of blood cells in patients with AML for immunotherapy. Based on our studies of inducing AML dendritic cell (AMLDC) differentiation and priming in situ AML-reactive T cells, we have developed a novel method of generating multiple autologous AML reactive T cell lines by limiting dilution AMLDC (LD-AMLDC) culture. The principle of LD-AMLDC is based on the assumption that autologous AML-reactive T cells or precursors are randomly distributed in the AML PBMC suspension, and that each one has an equal opportunity to respond to AML cells in the 96-well plates under optimized culture condition. By culturing AML PBMC (>90% blasts) in culture medium supplemented with GM-CSF/IL4/IL2/IL7/IL12 to induce AML DC differentiation and activate in situ autologous T cells, highly reactive anti-AML T cell lines (both CD4+ and CD8+ lines) were selected and expanded from LD-AMLDC culture using the appropriate numbers of AML PBMC in each culture well by the criterion of release of IFN-gamma in response to autologous AML blasts. By maximum likelihood solution, the estimated average frequency of AML reactive T cells or precursors is 6±3/1,000,000 AML PBMC (n=8). Strong intracellular IFN-gamma release of T cell lines obtained in LD-AMLDC was demonstrated by flow cytometry analysis after stimulation by autologous AML cells but not autologous B-lymphoblastoid cell line (LCL) (Figure). Effective specific lysis (up to 70% at E:T=20:1) of autologous AML cells but not autologous LCL or allogeneic AML cells by these T cell lines was observed. Two PR1 specific T cell lines were obtained by screening 39 AML reactive HLA-A2+ CD8+ T cell lines generated from 5 LD-AMLDC cultures, suggesting that other unidentified CD4 or CD8 lines with strong autologous AML responses may be reactive to known or unknown LAAs. These results encourage continued efforts to induce, activate and select T cells lines with high autologous AML reactivity using LD-AMLDC culture and to expand multi-LAA reactive T cell lines acquired from limiting dilution AML-DC culture for AML immunotherapy.
Figure Figure
The Expression of T Cell Receptor Signaling Genes Is Associated with Poor Response to IFN-α and/or PUVA in Mycosis Fungoides.
Authors: Wozniak Magdalena , Ortiz Pablo , Tracey Lorraine , Peralto Jose L. , Alvarez Monica , Piris Miguel A. , Villuendas Raquel 
Published: October 2019

Abstract
Mycosis fungoides (MF) is a low-grade cutaneous T-cell lymphoma, in which malignant T cell clones (mostly CD4+) arise in the skin from the early disease stages. IFN-α is widely used in the treatment of MF and when used in combination with PUVA has been reported as an effective treatment, with overall response rates of 30%–80%, and complete response rates of 14%–25%.
However, up to date there is no information available on prognostic factors that could help to predict response to IFN-α /PUVA in MF. The purpose of the study was to find the molecular signature associated with IFN-α /PUVA resistance, or lack of remission after IFN-α /PUVA treatment. The gene expression profile of the pre-treatment samples from 30 MF patients enrolled in a random clinical trial with IFN-α and/or PUVA has been analyzed by use of cDNA microarrays. Following the treatment outcome, the patients have been divided into good responders (23 patients that have achieved complete remission in the time of 24 weeks or less) and bad responders (7 patients that have not reached completed remission or have shown progression of the disease during treatment). The genes associated with good vs. bad response have been identified. Four genes associated with cell cycle regulation and tumour microenviroment have been identified to predict good response by the significance analysis of microarrays (SAM) correlating expression data with survival time. Moreover, 38 genes involved in T cell receptor signaling pathway, NF-kB activation and Jak-Stat signaling pathway have been found to be associated with unfavorable response to treatment by use of SAM analysis. This was validated using other bioinformatics tools based on t-statistics and Cox-model, applying False Discovery Rate for multiple testing. Furthermore, using a web-based tool (Signs) that uses a combination of gene filtering, clustering and survival model building, a 2-gene model has been obtained. This model could distinguish two groups of MF patients with probability of remission at 24 weeks of 15%, and 60% (log-rank test, p:0.007). This confirms that TCR-signaling plays a key role in cutaneous T-cell lymphoma cell survival; and could potentially be used for stratifying MF patients treated with IFN-α /PUVA into different risk-groups, if confirmed in additional studies.
The Oncogenic Fusionprotein NPM-ALK Cooperates with Bcl2 To Induce T-Cell Lymphomas in Mice.
Authors: Miething Cornelius , Grundler Rebekka , Mugler Claudia , Bauer Anette , Häcker Georg , Peschel Christian , Duyster Justus 
Published: October 2019

Abstract
The NPM-ALK fusion oncogene arising from the t(2;5) translocation has been shown to transform lymphoid cells in culture and induce tumors in mice. In a previous report, we have demonstrated that expression of NPM-ALK in a murine retroviral infection/transplantation model leads to histiocytic and plasmacytoid tumors in mice. In the earlier model, we did not find any signs of a T-cell malignancy in the transplanted animals, although control animals transplanted with an empty vector expressing EGFP demonstrated successful targeting of the T-cell compartment. To further delineate the effects of NPM-ALK expression in T-cells in cell culture, we infected a human T-cell line (Jurkat) with NPM-ALK. Interestingly, NPM-ALK expressing cells demonstrated an increased rate of apoptosis, whereas control infected cells showed normal growth without significant cell death. Bcl2 levels were reduced in the NPM-ALK expressing cells and exogenous Bcl2 expression could partially rescue NPM-ALK induced cell death. We therefore investigated the effect of increased Bcl2 expression in vivo by infection of either C57B6 wild type or vav-Bcl2 transgenic mice derived BM cells with NPM-ALK and subsequent transplantation into lethally irradiated recipient mice. Whereas the control mice mostly developed the previously described histiocytic malignancy without significant T-cell involvement, all mice receiving NPM-ALK and Bcl2 coexpressing cells displayed a thymus derived T-cell lymphoma with infiltration of the thymus, lymphnodes, spleen and to a lesser extent also the bone marrow, where the histiocytic phenoype predominated. The malignant T-cells expressed Thy1.2, CD4 and NPM-ALK, but were mostly TdT negative. Our results implicate that Bcl2 cooperates with NPM-ALK in the induction of T-cell lymphomas, suggesting that NPM-ALK may require additional hits to suppress apoptosis and induce full transformation in T-cells.
Genetics of t(11;14)(q13;q32)-Negative MCL.
Authors: Wlodarska Iwona , Vanhentenrijk Vera , Pospisilova Helena , Van Roosbroeck Katrien , Stul Michel , Minnei Francesca , Vandenberghe Peter , Verhoef Gregor , De Wolf-Peeters Chris 
Published: October 2019

Abstract
Mantle cell lymphoma (MCL) is hallmarked by IGH-mediated t(11;14)(q13;q32) resulting in deregulation of CCND1. This gene encodes cyclin D1 that together with cyclin D2 and -D3, plays a key role in cell cycle progression. Given that cyclin D1 is not expressed by normal B lymphocytes, its aberrant expression in lymphoma has a diagnostic value. Recently, it has been shown that rare cyclin D1-negative MCL cases express either cyclin D2 or cyclin D3. The molecular mechanisms underlying these events are unknown. We report here the genetic characteristics of 12 MCL cases without cytogenetic and FISH evidence of CCND1 rearrangement. These cases were collected over the last 15 years; they displayed the typical morphology and gene expression profile (determined by comparative expressed sequence hybridization) of MCL. Of interest, 5 of these lymphomas revealed cerebral or meningeal lesions at diagnosis or during a course of disease. Immunohistochemistry and RT-PCR studies showed a lack of expression of D-type cyclins in 2 cases. One of these cases was documented by t(2;14)(p24;q32) targeting NMYC, as shown by FISH and qRT-PCR. In this case upregulation of NMYC possibly led to inactivation of Rb and an aberrant progression of G1/S transition. The second case was characterized by a complex karyotype including loss of 17p. In the remaining 10 cases expression of cyclin D1, -D2 and -D3 in respectively 3, 2 and 5 cases was found. Cytogenetics and FISH identified t(2;12)(p11;p13) resulting in the IGK-CCND2 rearrangement in 1 of the 2 cases expressing cyclin D2 and der(14)t(6;14)(p21;q32) and der(20)t(14;20)(q32;p13) in one of the cases expressing cyclin D3. The breakpoint at 6p21 however was mapped distal to CCND3. FISH studies of p16, p27, p53 and Rb performed on all cases except one, identified loss of one copy of 1 to 4 of the analyzed genes in 7 cases. These data support the existence of t(11;14)-negative MCL that frequently express one of the three D-type cyclins. In one of the cases a new IG translocation affecting NMYC was found. Other genetic aberrations possibly involved in pathogenesis of t(11;14)-negative MCL included chromosomal translocations affecting CCND2 and unidentified genes at 6p21 and 20p13, and loss of tumor suppressor genes involved in cell cycle regulation.
Elevated Apurinic/Apyrimidinic Endonuclease Activity Significantly Contributes to DNA Instability in Multiple Myeloma.
Authors: Shammas Masood A. , Bertheau Robert C. , Koley Hemanta , Neri Paola , Tassone Pierfrancesco , Batchu Ramesh B. , Munshi Nikhil C. 
Published: October 2019

Abstract
Apurinic/apyrimidic (AP) sites are the commonest DNA damage lesions and are highly mutagenic and cytotoxic requiring immediate repair. AP endonucleases (APE) 1 and 2 are the key proteins involved in the repair of AP sites and therefore play an important role in maintaining genomic integrity. However, if APE activity is dysregulated, it may lead to increase in DNA breaks leading to genomic rearrangements. In this study we demonstrate that endonuclease activity as measured by a novel plasmid based assay is elevated over 5 fold in myeloma cell lines and primary myeloma cells relative to normal plasma cells. APE1 and 2 were identified as the major endonuclease in MM by gene expression profiling and protein studies as well as using methoxamine (MX), which specifically inhibits APE activity by reacting with the aldehyde group of an abasic site. To further investigate the role of elevated APE activity in MM, we cultured MM cells in the presence of MX and demonstrate a significant inhibition of DNA recombination activity, as well as acquisition of new mutations as assessed by change in genome-wide loss of heterozygosity (LOH) using the 100K single nucleotide polymorphism arrays. Conversely, in cell line with lower APE activity we demonstrate a significant increase in genomic rearrangement with acquisition of significant number of new LOH loci. These data suggest that dysregulated AP endonuclease activity plays an important role in ongoing accrual of mutational changes, which may be associated with progression of myeloma and/or development of drug resistance. Moreover APE1 and APE2 provide a novel target to prevent disease progression and drug resistant phenotype associated with genomic instability.