bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autoantibodies Specific to hnRNP K: A New Diagnostic Marker for Immune Pathophysiology in Bone Marrow Failure Syndromes.
Authors: Qi Zhirong , Takamatsu Hiroyuki , Lu Xuzhang , Espinoza J. Luis , Sugimori Naomi , Mochizuki Kanako , Nakao Shinji 
Published: April 2020

Abstract
The pathophysiology of bone marrow failure syndromes (BMS) such as aplastic anemia (AA) and refractory anemia (RA) of myelodysplastic syndromes defined by the FAB classification involves immune mediated bone marrow injury and intrinsic defects of hematopoietic stem cells. The diagnosis of the immune pathophysiology is essential in providing the optimal treatment to patients with BMS. In order to identify a new diagnostic marker for the immune pathophysiology of BMS, the sera of AA patients characterized by the presence of small populations of paroxysmal nocturnal hemoglobinuria-type (PNH) cells were screened for the presence of antibodies (Abs) recognizing proteins derived from a megakaryocytic leukemia cell line, UT-7. Two-dimensional electrophoresis of UT-7 lysates followed by immunoblotting revealed a distinct spot of 65 kDa. Peptide mass fingerprinting identified this protein as a heterogeneous nuclear ribonucleoprotein (hnRNP) K. Although hnRNP K is known to be ubiquitously expressed, the expression levels based on a Western blotting analysis were greater in several leukemia cell lines such as UT-7, K562 and OUN-1 in comparison to peripheral blood mononuclear cells. When the sera of newly diagnosed 87 BMS patients (62 with AA and 25 with RA) were examined for the presence of anti-hnRNP K Abs using an enzyme-linked immunosorbent assay (ELISA) with recombinant hnRNP K protein, significantly higher titers of anti-hnRNP K Abs were detected in 13 (34%, 10 with AA and 3 with RA) of 38 patients with BMS displaying increased PNH-type cells (PNH+) and in 15 (31%, 8 with AA and 7 with RA) of 49 patients without increased PNH-type cells. The presence of hnRNP K Abs was significantly correlated with the presence of anti-diazepam-binding inhibitor-related protein-1 (DRS-1) Abs (r=0.7206) and anti-moesin Abs (r=0.8318). Of the 87 patients, 49 patients (39 with AA and 10 with RA) received antithymocyte globulin plus cyclosporine therapy after the Ab screening. All of the 22 patients with high anti-hnRNP K Ab titers responded to therapy while 10 (37%) of 27 patients without the high titer Abs responded (P &lt; 0.005). When the three Ab titers were assessed, the response rate to immunosuppressive therapy in patients showing high titers in at least one Ab was 96%, while the response rate in patients not showing high titers in any of the auto-Abs was 39% (P &lt; 0.005). These findings suggest that in patients with immune mediated BMS, a breakdown of immune tolerance to multiple self antigens including hnRNP K may take place and that the detection of these auto-Abs may help diagnose the immune pathophysiology of BMS.
Depletion of the Shwachman-Diamond Syndrome Protein in Hematopoietic Progenitor Cells Impairs Growth, Colony Formation, and Ribosome Function.
Authors: Sezgin Gulay , Nihrane Abdallah , Ellis Steven , Liu Johnson M. 
Published: April 2020

Abstract
Shwachman-Diamond syndrome (SDS) is an autosomal recessive disorder characterized by pancreatic exocrine dysfunction, skeletal abnormalities, and bone marrow failure, which can evolve to leukemia. Mutations in SBDS have been shown to cause SDS. We and other investigators have suggested that SBDS orthologs in yeast play a role in biogenesis and function of the 60S ribosomal subunit. To clarify the unknown function of SBDS in hematopoiesis, human erythroleukemia TF-1 cells were transduced with lentiviral vectors expressing the green fluorescent protein (GFP), neomycin phosphotransferase, and small interfering RNA (siRNA) against SBDS. After transduction, cells were selected for neomycin resistance and then sorted by flow cytometry. To probe for SBDS, an antibody against the carboxyl-terminus of human SBDS was generated, and individual TF-1 cell clones expressing different siRNAs were confirmed to knock down SBDS expression by Western blot analysis. Our experiments were aimed at analyzing the cellular effects of SBDS knockdown. The growth and hematopoietic colony forming potential of TF-1 knockdown cells were markedly hindered when compared to cells stably transduced with siRNA against a scrambled SBDS sequence. Using propidium iodide staining and flow cytometric analysis, we found an increased percentage of knockdown cells retained at the G0/G1 cell cycle phase. To address whether TF-1 cells expressing siRNA against SBDS have a selective deficiency of 60S ribosomal subunits, cell extracts were prepared and polysome profiles examined after sucrose gradient centrifugation. In preliminary experiments, TF-1 cells expressing siRNA against SBDS appeared to show a reduction in free 60S subunits and 80S subunits with a shift toward smaller polysomes, compared to cells expressing the scrambled sequence siRNA. We conclude that depletion of SBDS results in a significant growth and clonogenic defect in TF-1 hematopoietic cells. Our preliminary results also suggest defects in ribosome function and cell cycle transit, which may provide an integrated molecular explanation for the hematopoietic defect in SDS since nucleolar stress has been linked to cell cycle arrest and p53 stabilization.
Genetic Abnormalities Involved in the Development and Progression of Follicular Lymphoma.
Authors: Deffenbacher Karen E , Wright George , Iqbal Javeed , Geng Huimin , O’Shea Derville , Lister T. Andrew , Fitzgibbon Jude , Fu Kai , Liu Zhongfeng , Weisenburger Dennis , Greiner Timothy C. , Gascoyne Randy D. , Rosenwald Andreas , Campo Elias , Rimsza Lisa M. , Delabie Jan , Jaffe Elaine S , Staudt Louis M. , Chan Wing C. 
Published: April 2020

Abstract
Background: Follicular lymphoma (FL) is the most common indolent B-cell lymphoma and remains incurable by current therapeutic approaches. Clinical course is variable, and transformation into an aggressive lymphoma (t-FL) with marked worsening of prognosis occurs in 20–60% of patients. While Bcl2 gene translocation is a critical initiating event in the majority of FL cases, evidence indicates it is not sufficient for the development of a FL. Characterization of the genetic alterations subsequent to Bcl2 translocation will lend insight into the oncogenic pathways that contribute to FL pathogenesis and the molecular mechanisms underlying variability in clinical course.
Methods: To define recurrent genomic copy number alterations (CNA) in FL, we performed high resolution array comparative genomic hybridization (aCGH) using the Affymetrix 500K SNP array platform. aCGH data were generated on a series of 112 FL cases with available gene expression profiling (GEP) and clinical information. Gene expression data were correlated with copy number data using the Gene Expression and Dosage Integrator (GEDI) algorithm developed at the NCI.
Results: Selecting for abnormalities occurring in &gt;10% of cases, the minimal common region (MCR) for 38 losses and 31 gains were defined. Novel common regions included gains on 15q11, 16p11, 5p14 and 19q13, and losses on 3q29, and 16p13. The MCR identified by aCGH were also compared with our existing cytogenetic data on 360 FL cases. MCR residing within the most frequent cytogenetic imbalances (&gt;5%) were selected for analysis at the gene level to further refine these regions. These include gains on 1q21, 2p16, 7q11, 8q24, 12q13, 17q21, 18q21, 21q11, and X, and losses on 1p36, 6q, 10q, 13q34, and 17p13. Recurrent amplifications were detected for the 2p16, 15q11, and 17q21 MCR, while frequent uniparental disomy (UPD) was found to overlap the region of loss on 1p36. Recurrent UPD was also noted on 6p, 12q, 15q and 16p. For the majority of selected MCR, global expression of the genes residing in the MCR demonstrated an association with copy number status. Within these abnormalities, individual genes showing significant correlation with copy number were also identified.
Conclusion: The combination of high resolution aCGH and GEP facilitated the identification of functionally relevant genes within the chromosomal abnormalities in FL. Delineation of these molecular targets will provide insight into the oncogenic pathways that contribute to FL disease pathogenesis and may provide novel therapeutic targets.
Inversely Association of the Aiolos Transcription Factor with Clinical Progression in Chronic Lymphocytic Leukemia.
Authors: Nückel Holger , Frey Ulrich H , Sellmann Ludger , Collins Crista H , Duehrsen Ulrich , Siffert Winfried 
Published: April 2020

Abstract
Introduction: Aiolos encode a hemopoietic-specific zinc-finger transcription factor that is an important regulator of lymphocyte differentiation and plays a critical role in regulating B-cell development. RT-PCR analysis of the Aiolos gene expression revealed 16 Aiolos splicing variants, which have been named according to the exons missing from the full-length isoform. Recent data suggest that over 80% of expressed Aiolos in normal as well as in malignant B-cells is of the hAio1 type. Therefore, we investigated Aiolos mRNA expression (hAio1 type) in a large cohort with 155 patients along with the most commonly used biological markers in order to assess its role in risk prediction in B-CLL.
Methods and Results: The total amount of Aiolos transcripts in B-cells of 155 CLL patients using normal peripheral blood mononuclear cells represented a continuum ranging from 2.5- to 37-fold upregulation compared to that of normal B-cells, with a median of 20- fold upregulation. Moreover, Aiolos expression in B-CLL was significantly upregulated compared to cells of AML (113-fold; p&lt;0.0001), ALL (14-fold; p=0.0024), CML (154- fold; p&lt;0.0001), multiple myeloma (38-fold; p=0.0018) or NHL (16-fold; p&lt;0.0001) suggesting that this Aiolos transcript is highly expressed specifically in B-CLL cells Patients with high Aiolos expression (according to ROC-analysis) had a significantly longer treatment-free survival (TFS) and overall survival (OS) than patients with low Aiolos expression (median TFS: 119 versus 45 months, p=0.005; median OS: 321 versus 244 months, p=0.0065). Evaluation of several disease characteristics in association with the Aiolos expression status of the patients’ B-CLL cells showed no significant differences for ZAP-70 expression (p=0.28), CD38 expression (p=0.067), IgVH status (p=0.49) and Binet stage (p=0.13) suggesting no correlation of Aiolos expression with these already established adverse prognostic factors. In multivariate analysis low Aiolos expression was an independent prognostic factor with significance for trend (hazard ratio 1.413; p=0.069). Sequential analyses in a subset of 10 CLL patients revealed that Aiolos expression was relatively stable over time in the majority of patients.
Conclusions: Here we demonstrate for the first time that the level of Aiolos expression is correlated with prognosis in B-CLL. The exact causes and consequences of this upregulation on the survival of CLL B-cells and the demonstrated better prognosis have yet to be determined. However, Aiolos may function as a tumor suppressor by controlling the cell cycle and DNA replication.
Overexpression of TOSO in CLL Is Triggered by B-Cell Receptor Signaling and Associated with Progressive Disease.
Authors: Pallasch Christian P , Schulz Alexandra , Kutsch Nadine , Schwamb Janine , Hagist Susanne , Wickenhauser Claudia , Ultsch Alfred , Kashkar Hamid , Hallek Michael , Wendtner Clemens-Martin 
Published: April 2020

Abstract
Resistance towards apoptotic stimuli mediated by overexpression of antiapoptotic factors or extracellular survival signals like B-cell receptor stimulation (BCR) are considered to be responsible for accumulation of malignant B cells in CLL . TOSO, also known as Fas-inhibitory molecule 3 (FAIM3), was identified as overexpressed candidate gene in CLL based on re-evaluation of publicly available microarray data sets. Based on primary CLL samples from 106 patients, TOSO expression was compared to healthy donor B cells using quantitative real-time PCR, western-blot, flow cytometry and immunohistochemistry. To reveal underlying mechanisms of TOSO overexpression, B-cell receptor (BCR) and CD40Ligand stimulation as well as bone marrow stroma cell co-incubation was performed. Apoptotic resistance was assessed by annexin V/7-AAD flow cytometry in context of CH11-Fas-agonistic antibody. TOSO was identified to exhibit elevated relative expression of 6.8 compared to healthy donor B cells using quantitative real-time PCR (p=0.004). High levels of TOSO expression in CLL correlated with high leukocyte count, advanced Binet stage, previous need for chemotherapy and unmutated IgVH status. CD38+ CLL subsets harboring proliferative activity showed significantly enhanced TOSO expression. Immunohistochemistry revealed upregulation of TOSO in lymph nodes of CLL patients. In lymph nodes derived from healthy donors TOSO was detected in single plasmocytoid cells within the germinal center and in the marginal zone. No specific staining was seen in follicular lymphomas. CLL-specific upregulation of TOSO was confirmed by RT-PCR, samples of follicular lymphomas, DLBCL, marginal zone lymphoma and Hodgkin cell lines did not reveal TOSO up-regulation. We evaluated functional mechanisms of aberrant TOSO expression in CLL cells and identified TOSO expression significantly being induced by BCR-stimulation compared to control cells (relative expression (RE) 8.25 vs. 4.86, p=0.013). In contrast, CD40L signaling significantly reduced TOSO expression (RE 2.60; p=0.007). Spontaneous apoptosis of CLL cells was significantly reduced by BCR-stimulus, in CD40Ligandstimulated CLL samples a slight sensitization towards Fas-mediated apoptosis was seen. In summary, we show that the anti-apoptotic factor TOSO is associated with progressive disease and enhanced in the proliferative CD38+ cell subset. Both association with unmutated IgVH and the specific induction of TOSO via the BCR suggest autoreactive BCR signaling as a key mediator of apoptosis resistance in CLL. Down-regulation of TOSO by CD40Ligand in the context of CD40Ligand-mediated Fas-sensitization of CLL reveal TOSO as a new anti-apoptotic factor in CLL. CLL-specific over-expression of the transmembrane protein might further offer new therapeutic strategies in CLL treatment.
Deregulation of Micrornas Results in Overexpression of Oncogenic Transcription Factors Involved in Pathogenesis of CLL.
Authors: Pallasch Christian P , Hagist Susanne , Patz Michaela , Schulz Alexandra , Debey Svenja , Eggle Daniela , Schultze Joachim L , Hallek Michael , Wendtner Clemens-Martin 
Published: April 2020

Abstract
MicroRNAs play a key role in the control of translation and mRNA degradation by binding to the 3′ untranslated regions of mRNAs. Immune cell development is especially dependent on miRNA regulation like miR-155 in germinal center development. Distinct miRNA-deregulation has been recently identified in CLL, however the proposed model of miR-15/16 mediated pathogenesis remains controversial. CLL cells of 50 treatment-naïve patients and peripheral B-cells of 14 healthy donors were separated by untouched depletion and processed for isolation of at least 200 ng total RNA. A new Illumina based Bead Chip was applied using 100 ng of total RNA for reliable hybridization. Target prediction of deregulated miRNAs was performed by in-silico predictions of miRNA-target gene interactions by TargetScan and PicTar. MiRNA target candidates were analyzed for differential protein expression in healthy donor B cells versus CLL cells. The applied technology was repetitively controlled and demonstrated to reveal reliable quantitative results. Comparing CLL samples with healthy donor B cells an overall decrease of miRNAs was observed in CLL samples. In total 19 miRNA were identified to be significantly lower expressed in CLL. 7 miRNAs were overexpressed in CLL. Comparing previously published data we could reliably identify upregulation of miR- 155 and downreguation of miR-181. However, the intensively discussed deregulation of miR-15 and miR-16 could not be verified. Furthermore we identified a so far not described CLL-specific miRNA-fingerprint of 26 miRNAs. Based on this fingerprint we analyzed for miRNA targets based on target prediction. A significantly focused number of transcription factors were identified by this primary screen. We could confirm predicted over-expression of oncogenic transcription factors by immunoblotting analysis. Targeting of deregulated miRNAs to 3′UTR of target genes was assessed by luciferase reporter assays. Decreased activity of 3’UTR-reporter construct was achieved by cotransfection with synthetic miRNAs together with target 3′UTRs. Targeted mutation of putative binding sites revealed an abrogation of miRNA-mediated suppression of luciferase activity confirming specificity of miRNA-3′UTR interaction of target genes. Here we could identify significant down-regulation of miRNA in CLL, a so far not identified cluster of deregulated miRNAs led to the identification of oncogenic transcription factors as novel target genes and pathogenic pathways in CLL. A key question remains regarding the cause of down-regulation of miRNAs mainly observed in CLL. Since no genomic hotspot is apparent, an impaired processing of pre-/pri-miRNAs or suppressive transcription factor loops have to be hypothesized and investigated to reveal the regulatory role of miRNA in malignant transformation of CLL.
Regulation of B-Cell Chronic Lymphocytic Leukaemia Cell Survival and Migration by the VEGF/SEMA3A Axis.
Authors: Murphy Philip T , Power Brendan p , Thornton Patrick D , Harmey Judith H 
Published: April 2020

Abstract
B-cell Chronic Lymphocytic Leukaemia (B-CLL) is characterized by the accumulation of B-CLL lymphocytes in the blood, marrow and secondary lymphoid tissues. B-CLL cells have a long survival owing to alterations in the normal pathways of apoptosis. In the marrow and lymphoid tissues CLL cells are in close contact with stromal cells that constitute distinct microenvironments. The secretion of the CXCR4 ligand, CXCL12, by stromal cells attracts B-CLL cells and provides protection from spontaneous or induced apoptosis. Studies in other cell types have shown VEGF signalling is involved in regulating CXCR4 expression levels.
The aim of this study was to examine VEGF receptor expression and the role of VEGF signalling in cell survival and CXCR4 expression. Expression levels of CXCR4 and VEGF receptors, VEGFR-1 and -2, in CLL samples were determined by flow cytometry. Expression of the VEGFR co-receptor, Neuropilin-1 (NRP1), was examined by Western blot. Cell migration towards CXCL12 was assessed using CoStar Transwell chambers (5mm pore size). Informed consent was received from all patients.
VEGFR1 and VEGFR2 positive cells in 22 patient samples ranged from 0–38% and 1.5–83% respectively. NRP1 expression was detected in all samples analysed thus far (n=6). The NRP1 ligand, SEMA3A, a competitive inhibitor of VEGF binding to NRP1, decreased CXCR4 expression in patient CLL cells (n=8, p&lt;0.05). This decrease in CXCR4 levels correlated with reduced migration of SEMA3A treated CLL cells towards CXCL12 (88 +/− 12.7% of control levels, n=8, p&lt;0.05). Treatment of CLL cells with the VEGFR signalling inhibitor SU5416 decreased CLL cell survival which correlated with VEGFR1 expression levels (n=16, R=0.745, p&lt;0.01) but not with VEGFR2 expression levels.
These results show that signalling through the VEGF co-receptor NRP1 plays an important role in regulating CXCR4 levels in CLL cells, as well as CLL cell migration along a CXCL12 gradient. Our results also suggest that VEGF signalling through VEGFR1 may be particularly important in regulating CLL cell survival. Thus, the VEGFR/NRP1 signalling pathway may represent an important therapeutic target in B-CLL.
High T-Cell Lymphoma Breakpoint 1 (TCL1) Levels Are Associated with Lack of Response and Inferior Outcome Following Fludarabine, Cyclophosphamide, Rituximab (FCR) Frontline Therapy in Patients with Chronic Lymphocytic Leukemia (CLL).
Authors: Schlette Ellen , Tam Constantine S. , Herling Marco , Bueso-Ramos Carlos , Wierda William , Ferrajoli Alessandra , O’Brien Susan , Keating Michael , Jones Dan 
Published: April 2020

Abstract
Body: Expression of the human oncogene TCL1 in transgenic mice produces B-cell tumors that resemble human CLL suggesting a role in B-cell tumorigenesis. TCL1 protein levels in CLL vary, with the highest expression seen in the pre-germinal center subtype which is also correlated with expression of ZAP70. We compare here TCL1 and ZAP70 as markers of response and progression following FCR front-line chemotherapy in a large cohort of patients (pts.).
Methods: Paraffin-embedded pre-treatment bone marrow specimens from 243 CLL pts. who received FCR as frontline therapy between 11/99 and 01/04 were evaluated for TCL1 expression by immunohistochemistry (IHC) using a mouse monoclonal antibody developed in our laboratory. A three-tier grading system (0–2) for expression levels was used. Data on ZAP70 expression (by IHC) and IgVH mutation status was available for 195 and 76 pts., respectively. The series was evaluated for the endpoints of complete response (CR) rates, CR duration, time to failure (TTF),and overall survival (OS) as previously defined (Tam et al., Blood 2008).
Results: 54 (22%) CLL cases expressed no or minimal TCL1 protein (graded as 0), while 143 (59%) cases showed dim/partial TCL1 expression (graded as 1), and 46 (19%) cases expressed moderate to strong TCL1 levels (graded as 2; Table 1). Heterogeneous intratumoral TCL1 expression was seen in a subset of cases, especially within proliferation centers. High TCL1 expression correlated with presenting features of advanced disease, including higher pre-treatment WBC counts (p=0.01), elevated serum beta-2 microglobulin (p=0.01) and unmutated IgVH genes (p = .0007).
Most significantly, high TCL1 expression levels predicted failure to attain a CR (p=0.038), shorter TTF (p=0.0003), and inferior OS (p=0.003) following FCR therapy. Although ZAP70 and TCL1 were positively correlated (R = 0.24), TCL(−) cases were found in both the ZAP70(+) and ZAP70(−) subsets. Expression of ZAP70 was also associated with shorter TTF (p=0.004), and OS (p=0.02) but not failure to attain a CR (p=0.93) after FCR therapy.
Conclusions: In CLL pts initially treated with FCR, strong TCL1 expression by IHC, unlike ZAP70, is predictor of failure to attain a CR and is a prognostic marker of inferior outcome.
TCL1 (n=243) versus ZAP70 (n=195) expression by IHC IHC ZAP(−) (n=75) IHC ZAP(+) (n=120) TCL1 0 (n=54) 23 21 1 (n=143) 47 69 2 (n=46) 5 30 Figure Figure