bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Expression Profiling of Persistent Polyclonal B-Cell Lymphocytosis Using Whole Genome Microarrays.
Authors: Lawrie Charles H. , Troussard Xavier , Mossafa Hossein , Hatton Chris 
Published: April 2020

Abstract
Persistent polyclonal B-cell lymphocytosis (PPBL) is a rare B-cell disorder characterised by elevated serum levels of polyclonal IgM and persistent lymphocytosis of often bi-nucleated B-cells. The molecular basis of this disorder however remains poorly understood. We therefore used whole genome expression microarrays (Affymetrix U133 plus2.0) to compare the gene expression profile of 14 cases of PPBL with normal lymphocyte populations (6 B cell (CD19+) and 3 T cell (CD3+) samples). PPBL patients (10 female, 4 male) had a median age of 43 (range 28–63) and all were smokers with an average lymphocyte count of 5.34 x 107/ml (range 3.7–9) at time of presentation. Eight of these cases had +i(3q) and eight cases exhibited PCC, four cases displayed both chromosomal abnormalities. Normal lymphocyte populations were obtained from two pools of 12 individuals and individual donors.
Microarray data were first RMA pre-processed and then expression levels of patient samples’ genes compared with levels of both normal B cell and T cell samples. ANOVA (P&lt;0.01) was used to identify differentially expressed genes. Thirty-six genes were found to be up-regulated and 157 genes were down-regulated in all patient samples by at least 2-fold.
Components of the AP-1 transcription complex (FOS, FOSB and JUN) were found to be highly up-regulated in all PPBL samples with an average of 7.2, 7.9 and 31.6 fold expression respectively. The cell cycle regulatory molecule CDC27 was also found to be up-regulated in all patient samples (8.8-fold). Down-regulated genes of interest included the B-cell specific transcription factor BACH2 (3-fold), tumor-suppressor SMAD4 (3.6-fold) and apoptotic genes DRAK1 (3-fold) and CAS (5-fold). These data are currently being validated by quantitative RT-PCR.
We propose that over-expression of AP-1 may have significance in PPBL as increased expression of components of AP-1 have previously been linked with lymphoproliferative disorders including Hodgkin’s lymphoma and splenic marginal zone lymphoma. The underlying reason for over-expression of AP-1 in PPBL remains unknown but two characteristic features of this disease could provide clues; firstly AP-1 up-regulation has been demonstrated to be tobacco-induced in animal models and secondly the LMP1 protein of EBV can result in constitutive expression of the AP-1 complex.
FLJ/P1 Is a New Mitochondrial Dehydrogenase Important in Respiration and Apoptosis.
Authors: Coignet Lionel J. , Johnson Timothy , Nganga Alain , Ghoshal Pushpankur , Houde Christiane , Dolce Jean , Ghosh Debashis , Singh Keshav 
Published: April 2020

Abstract
Leukemia is a neoplastic proliferation of cells of hematopoietic origin that arises following somatic mutation in a single hematopoietic stem cell, the progeny of which forms a clone of leukemia cells. Genetic alterations leading to leukemia transformation of a cell are often associated with major alterations of chromosomes that can be detected by studying cells of the leukemic clone in mitosis. One of these alterations is a chromosomal translocation that is often used to identify genes potentially involved in other type of rearrangements such as deletions. Abnormalities of chromosome band 13q14 occur in hematologic malignancies of all lineages and at all stages of differentiation. Unlike other chromosomal translocations, which are usually specific for a given lineage, the chromosomal translocation t(12;13)(p12;q14) has been observed in both B-cell and T-cell precursor acute lymphoblastic leukemia (ALL), in differentiated and undifferentiated acute myeloid leukemia (AML) and in chronic myeloid leukemia at progression to blast crisis (CML-BC). Recently, we have shown the presence of a myeloid- and lymphoid-specific breakpoint cluster regions within chromosome band 13q14 in acute leukemia (Genes Chromosome Cancer 25:222-229,1999). In addition, a new cell line has been established from one of the lymphoid cases, MUTZ5, that carries a single t(12;13) translocation (Leukemia15:1471-1474, 2001). The molecular characterization of this translocation led to the identification of a new gene, FLJ13639, that is disrupted and lost in the MUTZ5 cell line. This gene shares homologies with the large family of short-chain dehydrogenase reductase (SDR). Furthermore, three transcripts and proteins were found to be differentially expressed for this gene, where P1 is potentially the active form of dehydrogenase, while P2 and P3 are lacking the co-activator site. We previously reported that one of the consequences of the loss of FLJ13639 is the over-expression of CD24 that appears to provide leukemia cells with a proliferation and invasiveness advantage, as well as a certain degree of chemoresistance. In addition, data on patient samples indicated a correlation between survival and CD24High/FLJ/P1Low expression profile (Blood 106 (11), Nov 2005). We show that FLJ/P1 is a new mitochondrial protein that is important for the respiration and apoptosis processes. Restoration of the FLJ/P1 function induced CD24 down-regulation, decreased invasive potential as assessed by Matrigel assay and decreased chemoresistance. FLJ/P1 function restoration might represent a new potential therapy, that could, when combined with the assessment of FLJ/P1-CD234 expression profiles, allow the future development of personalized treatment.
Restoration of Rituximab Sensitivity in CD20 Negative B-Cell Lymphoma Cells; Epigenetic Change of CD20 Expression after Treatment of Rituximab.
Authors: Tomita Akihiro , Hiraga Junji , Kiyoi Hitoshi , Kinoshita Tomohiro , Naoe Tomoki 
Published: April 2020

Abstract
CD20 surface antigen is widely expressed on normal B-lineage cells and B-lymphoid malignant cells. Rituximab, which is a chimeric monoclonal antibody specifically recognizing CD20 surface antigen, works as a molecular targeting drug against CD20 positive lymphoid malignancies. Although combination chemotherapy with Rituximab has significantly improved the survival of CD20 positive lymphoma patients, CD20 negative tumor regression and transformation becomes a considerable problem. Recently, we have identified a patient with CD20(−) diffuse large B-cell lymphoma (DLBCL) transformed from CD20(+) follicular lymphoma after chemotherapies including Rituximab. Here we established RRBL1 (Rituximab resistant B-cell lymphoma 1) cells from this patient’s CD20(−) B-cell lymphoma cells, and analyzed the mechanisms of negative CD20 surface antigen expression. CD20 was not expressed as determined by immunoblotting and FACS analysis, and resistance to Rituximab was observed after cell culture analysis with/without Rituximab. Expression of wild type CD20 mRNA was confirmed by RT-PCR, and no genetic mutation in coding sequence or promoter region was observed. Quantitative RT-PCR showed that CD20 mRNA expression level was almost 100 times lower than that of CD20 positive B-cell lymphoma cells obtained from DLBCL patients. These data suggest that lower expression level of CD20 mRNA is closely related to the negative CD20 surface antigen expression, and the aberrant transcription regulation by epigenetic mechanisms can be anticipated. With these data, we thought that CD20 expression could be restored by modulating the transcription regulation. As we expected, CD20 protein re-expression was confirmed by enhancing CD20 mRNA expression after the treatment with specific molecular targeting drugs, and the sensitivity for the Rituximab was significantly restored. Chromatin immunoprecipitation assay suggested that recruitment of co-repressor complexes to CD20 promoter might be related to the regulation of CD20 expression.
Our data may provide us with a new therapeutic strategy, epigenetic therapy or differentiation therapy, combined with molecular targeting therapy using Rituximab, for Rituximab resistant CD20(−) B-cell malignancies.
Frequent Mutation of the PIK3CA Gene in Saudi Arabian Diffuse Large B-Cell Lymphoma.
Authors: Abubaker Jehad A. , Bavi Prashant P. , Al-Harbi Sayer , Atizado Valerie L. , Al-Dayel Fouad , Ezzat Adnan , Uddin Shahab , Al-Kuraya Khawla S. 
Published: April 2020

Abstract
Phosphotidylinositol 3′-kinases are lipid kinases that regulate signaling pathways involved in cell proliferation, adhesion, survival, motility, and are implicated to play an important oncogenic role in many cancer types. The PIK3CA gene encodes the p110α catalytic subunit of PI3K-like gene. Recently, high frequencies of PIK3CA somatic mutations have been detected in various kinds of human cancers notably colorectal, gastric, and breast cancers. It has also been shown that somatic mutations in the PIK3CA gene have been associated with a higher expression of p-AKT in certain cancers. However, the role of PIK3CA mutations in hematological malignancies has not been elucidated in detail. Therefore, we tested whether PIK3CA is subject to mutations in diffuse large B-cell lymphoma (DLBCL). Exons 9 and 20, encoding the highly conserved helical and kinase domains of PIK3CA, which account for 85% of somatic mutation in PIK3CA gene, were subjected to direct sequencing analysis in 219 cases of DLBCL. Somatic missense mutations were observed in 17 of 212 (8%) DLBCL cases. Out of which, 10 mutations (60%) occurred at codon 1047 in the kinase domain, which is one of the previously reported hot spot within the PIK3CA gene. Additionally, a silent polymorphism (T1025T) was found in one of the DLBCL sample. Moreover, activation of AKT was observed in 14 out of 17 (82%) of the DLBCL harboring PIK3CA mutations. Further, 9 out of 17 cases showed high level of pAKT. Additionally, 12 out of 17 DLBCL patients with PIK3CA mutations showed over-expression of the proliferative marker Ki-67. Expression of high level of pAKT was significantly correlated with over-expression of Ki-67 (p=0.0097). Overall survival in DLBCL cases harboring PIK3CA mutation showed poor survival as compared to the DLBCL cases lacking mutations though it was not statistically significant. These data indicate that mutations of PIK3CA play an oncogenic role in DLBCL tumors and argue for a role of PIK3CA targeting in treatment of DLBCL patients.
AML1/ETO-Mediated Lysozyme Repression Is Independently Relieved by Inhibitors of DNA Methylation and Histone Deacetylation.
Authors: Claus Rainer , Fliegauf Manfred , Stock Michael , Duque Jesus , Kolanczyk Mateusz , Lübbert Michael 
Published: April 2020

Abstract
The human lysozyme (LZM) gene, a marker gene for myeloid-specific development, is highly methylated in immature myeloid and in non-myeloid cells (all LZM-negative), and unmethylated in LZM-expressing mature phagocyte cells. Thus this gene provides an excellent model for investigating differentation-associated DNA methylation changes during myelopoiesis. There is now increasing evidence that LZM (containing five perfect consensus binding sites for AML1/RUNX1 in its 5′ region) is repressed by the AML1/ETO chimeric transcription factor (Fliegauf et al, Oncogene 23:9070–81, 2004), and this repression can be relieved by siRNA-mediated AML1/ETO depletion in AML1/ETO-positive Kasumi-1 cells (Dunne et al., Oncogene, 2006). Recently, AML1/ETO has also been implicated in gene-specific epigenetic repression of interleukin-3 (Liu et al, Cancer Res 65, 1277–84, 2005).
By extensive methylation analyses of the LZM gene including bisulfite sequencing, we now demonstrate marked demethylation in both the CpG-poor 5′ region and the exonic CpG island after treatment of Kasumi-1 cells with non-cytotoxic concentrations of the DNA methyltransferase (DNMT) inhibitor 5-aza-2′-deoxycytidine (5-azaCdR), which was not associated with cellular differentiation. By Northern blot analysis, LZM mRNA levels in Kasumi-1 cells but not in AML1/ETO-negative HL-60 and U-937 cell lines were specifically and independently upregulated upon treatment with 5-azaCdR and, to a lesser extent, with the histone deacetylase (HDAC) inhibitor Trichostatin A (TSA). Combined treatment with subliminal concentrations of 5-azaCdR and TSA applied in different schedules did not reveal synergistic effects on LZM transcription. Relative chromatin accessibility of the LZM 5′ region, as detected by “MspI protection” assay, and associated with partial demethylation in several myeloid cell lines, was increased in Kasumi-1 with 5-azaCdR-induced further DNA demethylation, but not by TSA. As shown by chromatin immunoprecitation, TSA increased the acetylation of histones H3 and H4 both in the 5′ flanking region and exonic CpG island. In a U-937 inducible model, antagonization of AML1/ETO-mediated repression of LZM was achieved by TSA, implying that the histone deacetylation in this region of the human LZM gene is mediated by AML1/ETO protein.
In conclusion, we demonstrate functional interactions between DNA methylation and histone modifications in mediating LZM gene repression which implicate AML1/ETO as one component involved in local chromatin remodelling. Interestingly, inhibitors of DNA methylation and histone deacetylation independently relieve repression of this CpG-poor gene in AML1/ETO-positive cells.
Expression of ED-B Fibronectin in Tissues from Human Hematologic Malignancies.
Authors: Sauer Stefanie , Hoffmann Jens , Menrad Andreas , Durkop Horst , Menssen Hans D. 
Published: April 2020

Abstract
Newly formed blood vessels in tissues infiltrated by hematologic malignancies or solid cancers are strikingly different from normal healthy counterparts. Notoriously, they are characterized by vascular shunts, uneven vessel diameters, and endothelial fenestrations. In addition, for the vast majority of solid cancers the extracellular matrix of such vessels was found to contain a type of fibronectin that has an extra-domain B (ED-B), which is expressed during embryonic development and during major tissue remodeling, but not in normal adult organs. The unique expression pattern attributed to ED-B suggests that it may be well suited for vascular targeting. Preliminary data has shown that ED-B expression may also be detected in hematologic malignancies. We have analyzed a large series of human samples of different hematological malignancies, non-malignant or reactive lymphatic conditions, and normal lymphatic and hematopoietic tissues for ED-B expression, using immunohistochemistry (IHC; mAbs BC1, L19, and the newly created MX1) on paraffin sections after steam pressure-based epitope recovery. Consistent with the data from solid tumors, ED-B expression was not detected in normal lymph nodes and lymphatic tissues. However, considerable but variable vessel-associated ED-B expression was detected in the following tissue samples of hematologic malignancies: 56/59 (95%) of Hodgkin lymphomas, 33/36 (91.7%) of DLBCLs, 32/33 (97%) of follicular lymphomas, 17/18 (94.4%) of mantle cell lymphomas, 14/15 (93.3%) of anaplastic large T cell lymphomas, 16/16 (100%) of multiple myelomas,13/14 (92.8%) of B-CLL samples, and in 5/6 (83.3%) samples from chronic myeloproliferative bone marrow, and in 3/3 (100%) from acute leukemia. Reactive lymph nodes (9/10; 90%) showed a faint ED-B expression in the vascular walls, whereas in hypertrophic tonsils (n=5) and healthy or reactive bone marrow (n=12) ED-B expression was rarely detected. Consistent with the literature, ED-B expression was not detected in tissue samples from normal lymph nodes (n=5). Immunofluorescence was used to identify co-localization of ED-B fibronectin and blood vessel-associated epitopes (eg CD34). Also, results will be presented from experiments in which lymphoma and leukemia animal models were treated with a novel IL2 immunocytokine specifically targeted to the ED-B fibronectin (L19-IL2). Preliminary results from these models suggest that hematopoietic malignancies contain ED-B+ vessels. Our study indicates the presence of vessel-associated ED-B in the vast majority of tissue samples from patients with varied hematologic malignancies, suggesting a potential approach for clinical investigation with targeted immunocytokines.
Lack of Increased Gene Promoter Methylation at Relapse in Acute Promyelocytic Leukemia (APL).
Authors: Zhou Da-Cheng , Thompson Reid , Kim Haesook , Greally John , Gallagher Robert 
Published: April 2020

Abstract
Increasing methylation of gene-regulatory DNA sequences has been associated with the progression of malignancies, and, in APL, the pathogenetic PML-RARα fusion gene has been associated with DNA methyltransferase activity, which might contribute to this process. We, therefore, hypothesized that promoter methylation levels would be increased in APL samples at disease relapse. Preliminary studies of a few CpG-enriched gene promoters, using highly quantitative pyrosequencing technology, demonstrated considerable individual-specific variation in DNA methylation. Hence, we used matched pretreatment and relapse bone marrow and/or peripheral blood samples with &gt;85% promyeloblasts after low-density gradient enrichment from 4 APL patients. High quality DNA was prepared from fresh samples by a guanidinium-cesium chloride gradient procedure. Global analysis of CpG-enriched DNA was performed by the HpaII tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay (Khulan, et al, Genome Res. 16, 1046Khulan, et al, Genome Res. 16, 2006), using a microarray representing the promoters of 24,000 human genes. The HELP assay relies upon a comparative genomic hybridization of HpaII (methylation-sensitive) versus MspI (methylation-insensitive) digested genomic DNA and is able to distinguish populations of methylated loci from hypomethylated (HO) loci. Based on the mean centered log ratio (MCLR) of HpaII/MpaI (Khulan, et al), there were negligible global changes in methylation between the 4 matched pretreatment and relapse samples. Using cut-off values to select for hypermethylated (HR) DNA (MCLR ≤0.0) and more completely HO DNA (MCLR ≥1.0) revealed some decrease in the ratio of HR:HO DNA at relapse in 3 of the 4 patients, primarily due to an increased fraction of HO DNA (see table).

We then assessed relapse-associated changes in methylation in 3,908 promoters in which the change from pretreatment to relapse was associated with p &lt;0.05 (paired t-tests) across all 4 data sets. A change from HO to HR was defined as a decrease in the MCLR by ≥2-fold in the relapse group; a change from HR to HO was the opposite, i.e., an increase in MCLR by ≥2-fold. There was a change from pretreatment HO to relapse HR for 563 loci (7.5% of effective HO promoters) and from pretreatment HR to relapse HO for 949 promoters (8.6% of effective promoters). More stringently, when promoters were selected for a change in MCLR from pretreatment HO ≥1.0 to relapse HR ≤0.0 or, conversely from pretreatment HR ≤0.0 to relapse HO ≥1.0, 40 and 82 promoters, respectively, were identified with p ≤0.05. These results indicate that changes in gene promoter methylation from pretreatment HR to relapse HO are more common than the reverse, and they are contrary to our pre-study hypothesis that increased global DNA methylation might be a major contributor to molecular progression processes in APL cells leading to clinical relapse.
Different Activation of WNT Signaling Pathway in B-Cell and T-Cell Acute Leukemias.
Authors: Sayitoglu Muge , Hatirnaz Ozden , Erbilgin Yucel , Atalar Fatmahan , Ozbek Ugur 
Published: April 2020

Abstract
WNT signaling pathway proteins function as hematopoietic growth factors and regulate proliferation in normal T-cell and B-cell development. Recent experimental evidence demonstrated that oncogenic transformation in leukemias of both lymphoid and myeloid lineages is dependent on WNT signaling. Not much is known about activation of WNT signaling pathway, its ligands and receptors in hematopoiesis and leukemia pathogenesis. To define its role in leukemia, we aimed to determine mRNA levels of the critical members of WNT pathway (WNT5A, WNT10B, FZ5, β catenin, APC, TCF-1 and LEF-1) by using quantitative real time PCR in acute lymphoblastic leukemia (ALL) patients (T-cell n=42, B-cell n=46 and pre B-cell n=30) and normal hematopoietic cells (bone marrow n=6, peripheral blood n=10, and CD19+ cells from peripheral blood). These genes expressed varying levels in B-cells, preB-cells and T-cells. In the B-cell leukemia patients, WNT5A was expressed notably (OR=58.05 CI 95% 1.63–1219.55, p&gt;0,001). WNT5A directs Ca++ dependent signaling by PKC and a G protein dependent manner which is an alternative pathway for beta-catenin mediated signaling. Also LEF-1 levels were higher in B-ALL patients and APC expression was down regulated when compared to normal tissue (OR=18.81 CI 95% 0.34–5703, p&gt;0.001 and OR=0.212 CI 95% 0.006–8.816, p=0.001, respectively). It is known that LEF-1 blocks APC mediated β catenin nuclear export and activates transcription of various transforming genes, including cyclin, D1, c-myc, MMP7, and LEF-1 itself. WNT5A or WNT10B proteins were not found to be up regulated in preB-ALL whereas APC and LEF-1 gene expressions were increased compared to normal hematopoietic cells (OR=32.97 CI 95% 0.27–1281, 38 p&gt;0.001 and OR=5.57 CI 95% 0.28–89.51, p=0.01, respectively). We found increased TCF-1 expression (7.4 fold) without any β catenin accumulation in T-ALL patients. It is known that TCF-1 in absence of β catenin functions as a tumor suppressor gene. WNT5A, APC and LEF-1 gene expression levels were also different between T-cell, B-cell and preB cell ALL cases. WNT5A expression had the highest levels in B-ALL compared to T-ALL cases, whereas the highest APC expression levels were observed in preB and T-ALL patients. Also LEF-1 expression levels were significantly different between preB and T-cell ALL patients. Taken together these results indicate that WNT signaling genes have abnormal expression and are active in acute lymphoblastic leukemia. This data suggests different WNT activation mechanisms exist in the leukemic transformation in different hematopoietic cells.