bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Analysis of Protein Expression Changes Induced by Geldanamycin in NPM-ALK Positive Lymphoma Cells by Functional Proteomics.
Authors: Schumacher Jonathan A. , Crockett David K. , Lin Zhaoshang , Elenitoba-Johnson Kojo S.J. , Lim Megan S. 
Published: October 2019

Abstract
A subset of anaplastic large cell lymphomas are characterized by the t(2;5)(p23;q35) chromosomal translocation. Fusion of the nucleophosmin (NPM) gene on chromosome 5q35 with the anaplastic lymphoma kinase (ALK) gene on chromosome 2p23 results in the constitutive expression of the NPM-ALK oncoprotein. Heat shock protein 90 (HSP90) is a molecular chaperone involved in the folding of a number of substrate proteins implicated in cancer. The list of known HSP90 client proteins is expanding and includes oncogenes, cell cycle-associated proteins, and kinases including NPM-ALK. The ansamycin-based anti-cancer drug, geldanamycin (GA) has been shown to inhibit HSP90 by interfering with its function as a molecular chaperone, resulting in ubiquitin-mediated proteasomal degradation of its client proteins. To date, the cellular effects of inhibition of HSP90 by GA remain largely uncharacterized. Here, we describe a functional proteomics approach to identify the differentially expressed proteins in NPM-ALK positive lymphoma cells exposed to GA. GA induced a dose- and time-dependent decrease in cell viability with an IC50 of 20μM, which was associated with a G2/M cell cycle arrest followed by caspase-3 mediated apoptosis. Equal amounts of total cell lysates from DMSO-control and GA-treated SUDHL-1 cells were labeled with either the light or heavy cleavable ICAT™ reagent. Samples were combined, digested with trypsin, and separated by strong cation exchange chromatography and avidin affinity chromatography. Peptides were subjected to liquid chromatography (LC), electrospray ionization (ESI) and tandem mass spectrometry (MS/MS). The resulting peptides were searched against the NCBI and Swiss-Prot databases using SEQUEST™ for protein identification and relative quantitation determined by XPRESS™. A total of 117 proteins were differentially expressed by greater than 1.5-fold of which 48 were overexpressed and 69 were underexpressed in GA-treated cells relative to control. The 48 overexpressed proteins included those that are involved in apoptosis, protein degradation, cell communication, and cell cycle regulation. Of the 69 underexpressed proteins, many included proteins involved in ubiquitin-proteasome function (proteasome beta 2 subunit, HSP90-organizing protein, CBL-C), cytokines (IL-14 precursor), and DNA repair. Notably, a number of previously reported targets of HSP90/70 (male germ cell-associated kinase and IL-26 precursor) were identified. Our results provide insights into the role of HSP90 in the pathogenesis of NPM-ALK positive lymphomas and demonstrate the diverse cellular functions that are deregulated as a consequence of HSP90 inhibition.
Expression of Activation-Induced Cytidine Deaminase and Transcripts of Immunoglobulin Variable Heavy Chains in Mature B-Cell Lines Lacking Immunoglobulin Protein Expression.
Authors: Matsuo Yoshinobu , Drexler Hans G. , Harashima Akira , Okochi Ayumi , Daibata Masanori , Takakuwa Tetsuya , Orita Kunzo 
Published: October 2019

Abstract
Expression of immunoglobulin (Ig) chains is a definitive marker of B-cell origin. Ig chains are generated during B-cell maturation by somatic rearrangement of Ig gene sequences. This rearrangement generally follows an orderly progression beginning with the heavy (H) chain genes and proceeding to the light (L) chain genes. The fact that Ig expression in B-cells generally reveals single L and H chains implies monoclonal cell expansion. Nevertheless, several exceptions have been reported, including double light chain positive cases. However, only little is known about mature B-cell malignancies lacking any Ig protein expression at all. In order to clarify the mechanisms of lacking any Ig protein expression in mature B-cell malignancies, we have analyzed the expression of activation-induced cytidine deaminase (AID), terminal deoxynucleotidyl transferase (TdT), recombination acting gene (RAG)-1 and RAG-2, transcription factors (TFs) and mRNA transcripts of Ig variable heavy (IgVH) chains using five both surface membrane (Sm) and cytoplasmic (Cy) Ig negative B-cell lines derived from acute lymphoblastic leukemia L3 type (ALL-L3), Burkitt’s lymphoma (BL) and pyothorax-associated lymphoma (PAL). BALM-9N and BALM-16 are ALL-L3, KATATA is BL, OPL-1 and OPL-3 are PAL-derived cell lines (EBV+). In cytogenetic analysis, t(8;14)(q24;q32) in BALM-9N and KATATA and t(8;22)(q24;q11) in BALM-16 were detected, respectively. Band 14q32 was not involved in the PAL cell lines. All cell lines showed rearrangement of IgH chain genes. Expression of RAG-1 and RAG-2 was variable, TdT was negative for all, AID was expressed in all cell lines except for PAL cell line OPL-3. The seven TFs BOB1/OBF1, E2A, IKAROS, OCT1, OCT2, PAX5 and PU1 were universally expressed at the mRNA level in all cell lines. Reverse transcriptase polymerase chain reaction elucidated the IgVH gene usage. BALM-9N = VH4; BALM-16 = VH2; KATATA = VH3; OPL-1 = VH3; OPL-3 = VH3. In summary, the present study demonstrates that Ig gene recombination, class switch recombination and somatic hypermutation machineries are not the cause for the lacking expression of both Sm/Cy Ig chains in mature B-cell malignancies. The lack of any Sm/Cy Ig expression in such mature B-cells may indicate rather a germinal center origin.
Acquirement of Rituximab Resistance Is Associated with the Development of Chemotherapy Resistance in B-Cell Lymphoma Cells: Evidence of Shared Pathways of Resistance between Chemotherapeutic Agents and Biological Therapies.
Authors: Olejniczak Scott H. , Hernandez Francisco J. , Czuczman Myron S. 
Published: October 2019

Abstract
Pre-clinical studies have demonstrated that rituximab triggers apoptotic signals in B-cell lymphoma cells upon biding to CD20 antigen. Downstream signaling events observed in lymphoma cells following in vitro exposure of rituximab or chemotherapy include: 1) activation of the intrinsic apoptotic pathway and 2) increased mitogen activated protein kinase (MAPK) activity. In addition, pre-clinical and clinical studies strongly suggest that rituximab may sensitize lymphoma cells to apoptotic effects of various drugs used to treat NHL. Despite its anti-tumor activity, many patients relapse after initial response to rituximab-based therapy and demonstrate variable degrees of rituximab resistance. To further study the impact of rituximab resistance in cellular responses to chemotherapy we developed several rituximab resistant cell lines (RRCL) derived from Raji, SU-DHL-4 and RL cells by exposing cells to escalating doses of rituximab with (4RH cells) or without (2R cells) human serum. The rituximab resistance of each RRCL was confirmed by immunological assays. Subsequently, lymphoma cells (parental and RRCL) were exposed to various chemotherapeutic agents (cisplatin, doxorubicin, paclitaxel, or vincristine) for up to 48 hours. Detection of cell death was determined by trypan blue and/or propidium iodine staining. Caspase-3 activity was measured by PhiPhi Lux G1D2 enzymatic cleavage. Bcl-2 expression was determined by Western blotting. Chemotherapy resistance to all agents tested was observed in RRCL when compared to parental Raji, SU-DHL-4 and RL cell lines. In addition, caspase-3 activity was lower in RRCL following chemotherapy exposure than in parental cell lines. A significantly lower percent of RRCL cells within sub-G0/G1 peaks in cell cycle histograms confirmed that RRCL were less sensitive to chemotherapy-induced apoptosis. Additionally, an increase in Bcl-2 expression was observed in RRCL when compared parental cell lines. Our data strongly suggest that chemotherapy resistance emerges concomitantly with the acquirement of rituximab resistance in lymphoma cells. Chronic exposure to rituximab appears to cause overexpression of Bcl-2, which likely renders RRCL less susceptible to the apoptotic effects of chemotherapy agents. Ongoing studies are aimed at identifying and overcoming rituximab/chemotherapy shared cellular pathways of resistance.
Allogeneic Stem Cell Transplantation for Children with Advanced Primary MDS: Results from the EWOG-MDS Study Group Employing a Pre-Transplant Preparative Regimen with Busulfan, Cyclophosphamide and Melphalan.
Authors: Niemeyer Charlotte Marie , Zecca Marco , Korthoff Elisabeth , Duffner Ulrich , Zintl Felix , Ebell Wolfram , Starý Jan , Dilloo Dagmar , Peters Christina , Schmugge Markus , Sedlacek Petr , Messina Chiara , van Heuvel Marry , Bergstraesser Eva , Trebo Monika , Noellke Peter , Locatelli Franco 
Published: October 2019

Abstract
MDS in children is a rare disorder characterized by dysplasia and defined genetic abnormalities. In most patients (pts) MDS arises without known predisposing conditions (primary MDS). Here, we report the results of 55 males and 30 females with advanced primary MDS enrolled in the prospective EWOG-MDS trial 97. Data were analysed according to the most advanced FAB-type prior to SCT: 32 pts were classified as RAEB, 40 as RAEB-t and 13 as myelodysplasia-related AML (MDR-AML). Median age at diagnosis was 9.5 yrs (0.1–17.6) and median time from diagnosis of advanced MDS to SCT 4 mo (0.5–31). Cytogenetics revealed monosomy 7 in 32 pts, trisomy 8 in 7, a complex karyotype in 9 and other abnormalities in 9; karyotype was normal in 26 pts and unknown in 2. 31 pts had received AML-like therapy prior to SCT. All pts were given an unmanipulated graft after condititioning with busulfan 16 mg/kg, cyclophosphamide 120 mg/kg and melphalan 140 mg/m. Source of stem cells was bone marrow in 56 pts, peripheral blood in 25, cord blood in 2 and unknown in 2. 36 pts were transplanted from an HLA-identical relative (MFD), 49 pts from an HLA-identical or 1-antigen disparate unrelated donor (UD). GVHD prophylaxis consisted of CSA alone for MFD, whereas recipients of a UD graft generally received CSA, methotrexate and anti-lymphocyte globulin. Two pts suffered graft failure. The cumulative incidence of grade II-IV acute GVHD and chronic GVHD was 40% (SE 5%) and 25% (SE 5%), respectively. 18 pts suffered transplant-related mortality (TRM), the cumulative incidence of TRM in pts grafted from a MFD or UD being 14 and 25%, respectively (p=n.s.). Presence of acute GVHD II-IV (p<0.01), spleen size at SCT ≥ 1 cm below the costal margin (p=0.03) and age ≥ 12 years (p=0.04) predicted an increased risk of TRM. 17 patients relapsed at a median of 12 mo after SCT (1–107). The 5-year probability of leukemia recurrence was 29%, with no difference between MFD and UD transplants. While the highest FAB type prior to SCT predicted relapse with a cumulative incidence rate increasing from RAEB (13%, SE 10%) to RAEB-t (24%, SE 11%) and MDR-AML (69%, SE 20%) (p=0.03), the use of intensive chemotherapy prior to SCT or blast percentage at SCT did not. With a median observation time after SCT of 29 months (6–107) the EFS at 5-years was 62% (SE 12%) and 39% (SE 11%) for pts given SCT from a MFD or an UD, respectively (p=n.s). These results indicate that a large proportion of pts with advanced MDS can be rescued by SCT. Disease recurrence remains the main cause of treatment failure. Intensive chemotherapy prior to SCT should not be routinely employed.
Improved Outcomes for Peripheral Blood Stem Cell Transplantation in Advanced Myelodysplastic Syndrome.
Authors: Solomon Scott R. , Childs Richard , Montero Aldemar , Sloand Elaine , Wisch Laura , Wehrlen Leslie , Barrett John 
Published: October 2019

Abstract
Allogeneic marrow or peripheral blood stem cell transplantation (PBSCT) is the only curative treatment for myelodysplastic syndrome (MDS). Historically, transplantation for MDS has produced long-term disease-free survival rates of 30–40%, partially due to high procedural mortality (~40%) in this patient population. Although transplant outcomes in younger patients with low-risk disease have been favorable, inferior results are seen in older patients and those with more advanced disease. Evidence suggests that the lower transplant-related mortality (TRM) and improved graft-versus-leukemia seen with PBSCT may translate into improved clinical outcomes for MDS patients. Forty-four patients, aged 12–73 years (median 50) received a PBSCT from a matched related sibling donor (MRD). Patients aged <55 years, without prohibitive comorbidity, received myeloablative conditioning consisting of total body irradiation and cyclophosphamide, followed by a T cell depleted allograft and scheduled post-transplant donor lymphocyte infusions (MST, n=23). Patients ineligible for an ablative transplant due to age or poor health received reduced intensity conditioning (fludarabine and cyclophosphamide, melphalan, or busulfan) followed by a T cell replete allograft (n=21). Six patients had low-risk MDS (RA/RARS), while the majority of patients (86%) had advanced disease (RAEB [9], RAEBT [6], AML [13], therapy-related MDS [10]). Median follow-up is 15.3 (range 2–82) months. Patients with therapy-related MDS had a significantly lower survival rate due to a very high risk of relapse (figure). The actuarial probabilities of overall survival (OS), disease-free survival (DFS), relapse, and TRM were 64%, 59%, 26%, and 23% for primary MDS patients, and 51%, 47%, 40%, and 25% for the whole cohort. Transplant-related mortality in patients under 50 years of age was 11% vs. 45% in patients ≥50 years (p=0.03). OS and DFS were significantly better in recipients of MST (64%, 57%) than in patients receiving reduced-intensity PBSCT (33%, 34%), due to a higher risk of relapse in the latter group (55% vs. 29%, p=0.10). In nineteen patients <50 years receiving MST, actuarial probability of OS, DFS, relapse, and TRM were 81%, 72%, 23%, and 7%, respectively. In summary, PBSCT yields superior outcomes for patients with primary MDS, even in patients in transformation to AML. The inferior outcomes seen in therapy-related MDS suggest alternative therapies are required for this patient population. Reduced intensity transplantation permits curative therapy for MDS patients not amenable to MST, but at the price of increased TRM and relapse in this older cohort.
Figure Figure
Gene Expression Analysis of Peripheral T-Cell Lymphoma Not Otherwise Specified Reveals the Existance of Two Subgroups Related to Different Cellular Counterparts and Recurrent PDGFRA Deregulation.
Authors: Piccaluga Pier-Paolo , Agostinelli Claudio , Zupo Simona , Califano Andrea , Went Philip , Ascani Stefano , Basso Katia , Facchetti Fabio , Falini Brunangelo , Ferrarini Manlio , Gallamini Andrea , Klein Ulf , Novero Domenico , Paulli Marco , Tura Sante , Zinzani Pier Luigi , Baccarani Michele , Dalla-Favera Riccardo , Pileri Stefano A. 
Published: October 2019

Abstract
Peripheral T-cell lymphoma not otherwise specified (PTCL/NOS) is a rare non Hodgkin lymphoma characterized by heterogeneous morphologic and phenotypic features, aggressive clinical behavior, poor response to conventional treatments and dismal prognosis. Its molecular basis and relationships to normal T-cells are still unclear. We performed gene expression profiling of 17 PTCL/NOS cases, collected at diagnosis before any treatment, and 20 samples of normal T-lymphocytes. The comparison of the gene expression profiles of PTCL/NOS and purified normal T-cell subpopulations, including CD4+, CD8+, resting (HLA-DR-), and activated (HLA-DR+) elements, shows that PTCLs/NOS are more related to activated peripheral T-lymphocytes either CD4+ or CD8+, suggesting derivation from these compartments. Notably, immunohistochemistry on routine sections by using anti-CD4 and CD8 antibodies does not vicariate molecular analysis, as there is no correspondence between the global gene expression profile and CD4/CD8 antigen positivity. When compared with normal T-cells, PTCLs/NOS displayed a remarkable deregulation of functional programs often involved in tumorigenesis, such as apoptosis, proliferation, cell adhesion, and matrix remodeling. In addition, our analyses identified several genes that are specifically expressed in PTCLs/NOS. Their expression was confirmed at the protein level by immunohistochemical analysis of tissue micro-arrays including 160 primary PTCL/NOS cases. We applied several different markers that provided significant information as concerns the ectopic, paraphysiologic or stromal expression of the proteins corresponding to the deregulated genes. Among others, PTCLs/NOS aberrantly express CYR61, a molecule involved in drug resistance, and PDGFRA, a tyrosine kinase receptor whose deregulation is often related to a malignant phenotype. Notably, we demonstrated the constitutive activation of PDGFRA in the majority of cases - as indicated by its phosphorylation. Finally, we showed that imatinib mesylate significantly reduces PTCL/NOS primary cells viability after in vitro exposure at 1 mM concentration, independently from their sensitivity to conventional cytotoxic agents. These results are provided with biological implications relevant to the pathogenesis of the tumor, as well as for its clinical management.
Androgen Modulates Thymopoiesis by Regulating Thymocyte Precursor Immigration.
Authors: Williams Kirsten M. , Chu Yu-Waye , Gress Ronald E. 
Published: October 2019

Abstract
Impaired thymopoiesis contributes to immune deficiency in aging, AIDS, and following allogeneic bone marrow transplantation. However, little is known of the mechanisms of thymic regulation and the determinants of thymic function. Exogenous administration of testosterone and estrogen has been shown to accelerate thymic involution. Conversely, studies have demonstrated that castration of male mice resulted in increased thymic size and thymocyte number. We present data that thymic enlargement in castrated male mice is due to enhanced thymopoiesis. Comparing castrated post-pubertal male mice with age-matched control littermates, we found a statistically significant doubling of thymic weight, thymocyte number, and double-positive CD4+CD8+ thymocytes as early as eight days post-orchiectomy. Major thymocyte subsets defined as CD4− CD8−, CD4+CD8−, CD8+CD4− were also increased post castration and the ratio of subsets was unchanged suggesting that castration augmented overall thymic activity. This was further corroborated by a concomitant 4–6 fold increase in thymic T cell-receptor excision circles (TREC). Significantly, at one month post-castration, early thymic progenitors (Lin- CKIT hi CD44 hi) were increased threefold in the castrated cohort. The increase in thymic productivity led to a subsequent increase in peripheral cell populations, with a significant increase in splenic CD4+ and CD8+ T cells. The greatest proportion of this increase was due to naïve splenic CD4 and CD8 T cells total numbers as defined by CD44lo expression. Memory splenocytes, CD44hi CD4+ and CD8+ cells, were slightly increased as well. Additionally, there was an increase in the number of splenic recent thymic emigrants (RTE) as enumerated by TREC. Our data suggest that androgen withdrawal leads to an increase in thymopoiesis, as enumerated by a significant influx of ETPs, increased total thymic TREC, subsequent increases in single positive thymocytes, and increased peripheral recent thymic emigrants. Furthermore, the data suggest that a mechanism by which this occurs is through increased immigration of thymocyte precursors from the bone marrow into the thymus identifying this as a central point in thymic regulation.
Blocking Complement-Mediated Hemolysis Using RNA Aptamers That Bind Complement Component C8.
Authors: Nishimura Jun-ichi , Nimjee Shahid M. , Jiang Haixiang , Howard Thad A. , Pitoc George A. , Rusconi Christopher P. , Omine Mitsuhiro , Chao Nelson J. , Frank Michael M. , Sullenger Bruce A. , Ware Russell E. 
Published: October 2019

Abstract
A recent pilot study in patients with paroxysmal nocturnal hemoglobinuria (PNH), using a humanized monoclonal antibody that binds human complement C5 and inhibits terminal complement protein activation, suggests that blocking complement is a potentially effective therapeutic option for PNH. However, since C5 is critical for proper regulation of inflammatory responses as well as complement activation, terminal complement proteins with more restricted function may represent better targets. The pore-forming C5-9 complex includes several protein targets, but persons with C9 deficiency have measurable evidence of in vitro complement activation, indicating that the C5b-8 complex can cause lysis in the absence of C9. Blocking complement at C9 may not, therefore, completely prevent complement-mediated hemolysis and adequately protect PNH erythrocytes. Accordingly, we used in vitro selection methodology to identify high affinity nuclease-resistant RNA aptamers that bind specifically to human complement C8. Aptamers bound C8 with a Kd of 1.4nM and 54.1% after round 7. C8 aptamers identified after rounds 4 to 7 of selection were cloned and sequenced, and aptamer clones were screened for in vitro binding and complement-inhibitory activity. Aptamers were first incubated with purified C8 at a concentration sufficient to induce 50–70% hemolysis, then antibody-sensitized erythrocytes and C8-depleted serum were added. One C8 aptamer clone (4–101) had strong inhibitory hemolytic activity with 91.9% inhibition at 250nM, compared to only 12.3% inhibition observed with random aptamers at 250nM. Aptamer clone 4–101 bound C8 with a Kd of 15nM and a Bmax of 74.2%. Inhibition of hemolysis by C8 aptamer clone 4–101 was enhanced by adding a previously published C5 aptamer clone f8/c11, (TCTCATGCGCCGAGTGTGAGTTTACCTTCGT, Immunopharmacology42:219, 1999) in a modified human serum hemolytic assay using total human serum: 54.4% inhibition was observed using C8 aptamer 4–101 at 500nM, versus 83.0% inhibition using C8 aptamer 4–101 with C5 aptamer f8/c11 in combination at 500nM. Thus, C8 aptamer clones can efficiently inhibit complement-mediated lysis, with enhanced activity in combination with a known C5 aptamer. These data indicate that combinatorial blocking aptamers that bind terminal human complement proteins can efficiently inhibit the complement pathway, and therefore represent a novel potential therapeutic option for patients with PNH. Based on these in vitro data, therapeutic C8 aptamers should be considered for the in vivo treatment of PNH patients with massive hemolysis. C5 inhibitors could still be useful, however, as an adjunct therapy if C8 aptamers insufficiently inhibit complement-mediated lysis.