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https://www.readbyqxmd.com/read/27788226/identification-of-immunoglobulin-gene-sequences-from-a-small-read-number-of-mrna-seq-using-hybridomas
#1
Yuki Kuniyoshi, Kazumitsu Maehara, Takeshi Iwasaki, Masayasu Hayashi, Yuichiro Semba, Masatoshi Fujita, Yuko Sato, Hiroshi Kimura, Akihito Harada, Yasuyuki Ohkawa
Identification of immunoglobulin genes in hybridomas is essential for producing antibodies for research and clinical applications. A couple of methods such as RACE and degenerative PCR have been developed for determination of the Igh and Igl/Igk coding sequences (CDSs) but it has been difficult to process a number of hybridomas both with accuracy and rapidness. Here, we propose a new strategy for antibody sequence determination by mRNA-seq of hybridomas. We demonstrated that hybridomas highly expressed the Igh and Igl/Igk genes and that de novo transcriptome assembly using mRNA-seq data enabled identification of the CDS of both Igh and Igl/Igk accurately...
2016: PloS One
https://www.readbyqxmd.com/read/27614734/combined-ikzf1-and-ig-markers-as-new-tools-for-diagnosis-and-minimal-residual-disease-assessment-in-tunisian-b-all
#2
Sawsen Besbes, Walid-Sabri Hamadou, Marie-Laure Boulland, Marie-Paule Lefranc, Yosra Ben Youssef, Béchir Achour, Abderrahim Khelif, Thierry Fest, Zohra Soua
INTRODUCTION: The monitoring of minimal residual disease (MRD) approach in patients diagnosed with B-acute lymphoblastic leukemia (B-ALL) allows an early detection of residual clones inducing relapses and therefore appropriate therapy strategy. The molecular markers may identify and quantify the residual blasts in B-ALL with normal cytology. In this study, we aimed to use combined IKZF1, IGH and IGK immunoglobulin genes for diagnosis and MRD monitoring in B-ALL sample using MLPA, multiplex PCR and real-time quantitative PCR...
September 7, 2016: Bulletin du Cancer
https://www.readbyqxmd.com/read/27439714/identification-of-multi-loci-hubs-from-4c-seq-demonstrates-the-functional-importance-of-simultaneous-interactions
#3
Tingting Jiang, Ramya Raviram, Valentina Snetkova, Pedro P Rocha, Charlotte Proudhon, Sana Badri, Richard Bonneau, Jane A Skok, Yuval Kluger
Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these...
October 14, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27301320/collagen-epitope-expression-on-b-cells-is-sufficient-to-confer-tolerance-to-collagen-induced-arthritis
#4
Sofia E M Andersson, Tove Eneljung, Sara Tengvall, Pernilla Jirholt, Anna Stern, Louise Henningsson, Bibo Liang, Katrin Thorarinsdottir, Jan Kihlberg, Rikard Holmdahl, Inga-Lill Mårtensson, Kenth Gustafsson, Inger Gjertsson
BACKGROUND: The mechanisms underlying tolerance induction and maintenance in autoimmune arthritis remain elusive. In a mouse model of rheumatoid arthritis, collagen type II (CII)-induced arthritis, we explore the contribution of B cells to antigen-specific tolerance. METHODS: To generate expression of the CII-peptide specifically on B-cell major histocompatibility complex type II, lentiviral-based gene therapy including a B-cell-specific Igk promoter was used. RESULTS: Presentation of the CII-peptide on B cells significantly reduced the frequency and severity of arthritis as well as the serum levels of CII -specific IgG antibodies...
2016: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/27261530/molecular-functions-of-the-transcription-factors-e2a-and-e2-2-in-controlling-germinal-center-b-cell-and-plasma-cell-development
#5
Miriam Wöhner, Hiromi Tagoh, Ivan Bilic, Markus Jaritz, Daniela Kostanova Poliakova, Maria Fischer, Meinrad Busslinger
E2A is an essential regulator of early B cell development. Here, we have demonstrated that E2A together with E2-2 controlled germinal center (GC) B cell and plasma cell development. As shown by the identification of regulated E2A,E2-2 target genes in activated B cells, these E-proteins directly activated genes with important functions in GC B cells and plasma cells by inducing and maintaining DNase I hypersensitive sites. Through binding to multiple enhancers in the Igh 3' regulatory region and Aicda locus, E-proteins regulated class switch recombination by inducing both Igh germline transcription and AID expression...
June 27, 2016: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/27239026/active-and-inactive-enhancers-cooperate-to-exert-localized-and-long-range-control-of-gene-regulation
#6
Charlotte Proudhon, Valentina Snetkova, Ramya Raviram, Camille Lobry, Sana Badri, Tingting Jiang, Bingtao Hao, Thomas Trimarchi, Yuval Kluger, Iannis Aifantis, Richard Bonneau, Jane A Skok
V(D)J recombination relies on the presence of proximal enhancers that activate the antigen receptor (AgR) loci in a lineage- and stage-specific manner. Unexpectedly, we find that both active and inactive AgR enhancers cooperate to disseminate their effects in a localized and long-range manner. Here, we demonstrate the importance of short-range contacts between active enhancers that constitute an Igk super-enhancer in B cells. Deletion of one element reduces the interaction frequency between other enhancers in the hub, which compromises the transcriptional output of each component...
June 7, 2016: Cell Reports
https://www.readbyqxmd.com/read/27212160/ascites-as-the-initial-characteristic-manifestation-in-a-patient-with-primary-gastric-cd8-positive-diffuse-large-b-cell-lymphoma
#7
K-X Zhao, G-Z Dai, J-F Zhu
CASE PRESENTATION: Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid malignancy and the most common type of non-Hodgkin's lymphomas, the stomach is the most common extranodal site. Gastric DLBCL is often characterized by epigastric pain and vomiting. We report a case of a 78-year-old female patient with gastric diffuse large B-cell lymphoma (DLBCL) with high CD8 level which was initially manifested with ascites of unknown origin. The patient was admitted with a chief complaint of abdominal distension and scanty urine over the last twenty days, while without anorexia and fatigue until 15 March...
May 2016: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/27169754/molecular-clonality-assessment-shows-high-performance-to-predict-malignant-b-cell-non-hodgkin-s-lymphoma-using-cytological-smears
#8
Paul Roepman, Cecile-Marie Boots, Karen C Scheidel, Tobias Sprong, Peter de Bruin, Okke de Weerdt, Patricia J T A Groenen, J Alain Kummer
AIMS: Molecular PCR-based clonality analysis is helpful for identification of monoclonal B-cell or T-cell populations and to distinguish malignant lymphoma from reactive lymphoid hyperplasia. Typically, clonality assessment on fine-needle aspiration cytology (FNAC) requires freshly obtained aspirates, but the collection and processing of these samples are often challenging in daily practice. In this study, we assessed the routine diagnostic value of the EuroClonality/BIOMED-2 assay for B-cell clonality on air-dried archived Giemsa-stained smears...
May 11, 2016: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/27150991/-application-of-combined-detection-of-fusion-gene-and-biomed-2-standardized-ig-gene-rearrangement-system-in-childhood-b-cell-acute-lymphoblastic-leukemia
#9
Xiao-Fei Ai, Yan Zhang, Xin-Rong Shi, Ying-Chun Zheng, Li Zhang, Xiao-Jing Wang, Qing-Hua Li
OBJECTIVE: To explore the application of combined detection of fusion gene and BIOMED-2 standardized immunoglobulin (Ig) gene rearrangement system in diagnosis and treatment of children with acute lymphoblastic leukemia (ALL). METHODS: Multiplex-PCR amplifications and RQ-PCR of RNA/DNA were performed using ALL fusion gene detection kit and BIOMED-2 primer. The Ig gene rearrangements were analyzed by using PCR fragment analysis system. RESULTS: Out of 251 children with B-ALL, 77 cases were TEL-AML1(+) , 28 cases were E2A-PBX1(+) , 10 cases were MLL-AF4(+) , 11 cases were BCR-ABL(+) , the total positive rate was 50...
April 2016: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/27123263/immunoglobulin-gene-translocations-in-chronic-lymphocytic-leukemia-a-report-of-35-patients-and-review-of-the-literature
#10
Marc DE Braekeleer, Corine Tous, Nadia Guéganic, Marie-Josée LE Bris, Audrey Basinko, Frédéric Morel, Nathalie Douet-Guilbert
Chronic lymphocytic leukemia (CLL) represents the most common hematological malignancy in Western countries, with a highly heterogeneous clinical course and prognosis. Translocations involving the immunoglobulin (IG) genes are regularly identified. From 2000 to 2014, we identified an IG gene translocation in 18 of the 396 patients investigated at diagnosis (4.6%) and in 17 of the 275 analyzed during follow-up (6.2%). A total of 4 patients in whom the IG translocation was identified at follow-up did not carry the translocation at diagnosis...
May 2016: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/27122311/redox-proteomic-analysis-of-serum-from-aortic-anerurysm-patients-insights-on-oxidation-of-specific-protein-target
#11
Cristiano Spadaccio, Raffaella Coccia, Marzia Perluigi, Gilda Pupo, Maria Eugenia Schininà, Alessandra Giorgi, Carla Blarzino, Francesco Nappi, Fraser W Sutherland, Massimo Chello, Fabio Di Domenico
OBJECTIVES: oxidative stress is undoubtedly one of the main players in abdominal aortic aneurysm (AAA) pathophysiology. Recent studies in AAA patients reported an increase in the indices of oxidative damage at the tissue level and in biological fluids coupled with the loss of counter-regulatory mechanisms of protection from oxidative stress. We recently reported, in a proteomic analysis of AAA patient sera, changes in the expression of several proteins exerting important modulatory activities on cellular proliferation, differentiation and response to damage...
June 21, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27116572/enhanced-recombinant-factor-vii-expression-in-chinese-hamster-ovary-cells-by-optimizing-signal-peptides-and-fed-batch-medium
#12
Lin Peng, Xiao Yu, Chengyuan Li, Yanfei Cai, Yun Chen, Yang He, Jianfeng Yang, Jian Jin, Huazhong Li
Signal peptides play an important role in directing and efficiently transporting secretory proteins to their proper locations in the endoplasmic reticulum of mammalian cells. The aim of this study was to enhance the expression of recombinant coagulation factor VII (rFVII) in CHO cells by optimizing the signal peptides and type of fed-batch culture medium used. Five sub-clones (O2, I3, H3, G2 and M3) with different signal peptide were selected by western blot (WB) analysis and used for suspension culture. We compared rFVII expression levels of 5 sub-clones and found that the highest rFVII expression level was obtained with the IgK signal peptide instead of Ori, the native signal peptide of rFVII...
April 2016: Bioengineered
https://www.readbyqxmd.com/read/27025770/computational-deconvolution-of-gene-expression-by-individual-host-cellular-subsets-from-microarray-analyses-of-complex-parasite-infected-whole-tissues
#13
Nirad Banskota, Justin I Odegaard, Gabriel Rinaldi, Michael H Hsieh
Analyses of whole organs from parasite-infected animals can reveal the entirety of the host tissue transcriptome, but conventional approaches make it difficult to dissect out the contributions of individual cellular subsets to observed gene expression. Computational deconvolution of gene expression data may be one solution to this problem. We tested this potential solution by deconvoluting whole bladder gene expression microarray data derived from a model of experimental urogenital schistosomiasis. A supervised technique was used to group B-cell and T-cell related genes based on their cell types, with a semi-supervised technique to calculate the proportions of urothelial cells...
June 2016: International Journal for Parasitology
https://www.readbyqxmd.com/read/26898266/multi-loci-diagnosis-of-acute-lymphoblastic-leukaemia-with-high-throughput-sequencing-and-bioinformatics-analysis
#14
Yann Ferret, Aurélie Caillault, Shéhérazade Sebda, Marc Duez, Nathalie Grardel, Nicolas Duployez, Céline Villenet, Martin Figeac, Claude Preudhomme, Mikaël Salson, Mathieu Giraud
High-throughput sequencing (HTS) is considered a technical revolution that has improved our knowledge of lymphoid and autoimmune diseases, changing our approach to leukaemia both at diagnosis and during follow-up. As part of an immunoglobulin/T cell receptor-based minimal residual disease (MRD) assessment of acute lymphoblastic leukaemia patients, we assessed the performance and feasibility of the replacement of the first steps of the approach based on DNA isolation and Sanger sequencing, using a HTS protocol combined with bioinformatics analysis and visualization using the Vidjil software...
May 2016: British Journal of Haematology
https://www.readbyqxmd.com/read/26779602/multifunctional-role-of-the-transcription-factor-blimp-1-in-coordinating-plasma-cell-differentiation
#15
Martina Minnich, Hiromi Tagoh, Peter Bönelt, Elin Axelsson, Maria Fischer, Beatriz Cebolla, Alexander Tarakhovsky, Stephen L Nutt, Markus Jaritz, Meinrad Busslinger
The transcription factor Blimp-1 is necessary for the generation of plasma cells. Here we studied its functions in plasmablast differentiation by identifying regulated Blimp-1 target genes. Blimp-1 promoted the migration and adhesion of plasmablasts. It directly repressed genes encoding several transcription factors and Aicda (which encodes the cytidine deaminase AID) and thus silenced B cell-specific gene expression, antigen presentation and class-switch recombination in plasmablasts. It directly activated genes, which led to increased expression of the plasma cell regulator IRF4 and proteins involved in immunoglobulin secretion...
March 2016: Nature Immunology
https://www.readbyqxmd.com/read/26658664/primary-cutaneous-follicle-center-lymphomas-expressing-bcl2-protein-frequently-harbor-bcl2-gene-break-and-may-present-1p36-deletion-a-study-of-20-cases
#16
Vanessa Szablewski, Saskia Ingen-Housz-Oro, Maryse Baia, Marie-Helene Delfau-Larue, Christiane Copie-Bergman, Nicolas Ortonne
The classification of cutaneous follicular lymphoma (CFL) into primary cutaneous follicle center lymphoma (PCFCL) or secondary cutaneous follicular lymphoma (SCFL) is challenging. SCFL is suspected when tumor cells express BCL2 protein, reflecting a BCL2 translocation. However, BCL2 expression is difficult to assess in CFLs because of numerous BCL2+ reactive T cells. To investigate these issues and to further characterize PCFCL, we studied a series of 25 CFLs without any extracutaneous disease at diagnosis, selected on the basis of BCL2 protein expression using 2 BCL2 antibodies (clones 124 and E17) and BOB1/BCL2 double immunostaining...
January 2016: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/26632463/-application-of-biomed-2-standardized-ig-gene-rearrangement-system-in-multiple-myeloma
#17
Xiaofei Ai, Xiaojing Wang, Bo Wang, Shenghua Chen, Jun Wang, Qinghua Li, Gang An, Kun Ru
OBJECTIVE: To explore the application of BIOMED- 2 standardized immunoglobulin (Ig) gene rearrangement system in the diagnosis of multiple myeloma (MM), and the significance of clonality analysis by multiplex-PCR amplifications. METHODS: A total of 167 cases of MM bone marrow samples from 2009 to 2013, and 20 cases of reactive plasmacytosis used as the controls were included in this study. Multiplex-PCR amplifications were performed and the Ig gene rearrangements were analyzed using BIOMED-2 standardized clonality analysis system...
November 2015: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
https://www.readbyqxmd.com/read/26608917/the-dna-ligase-iv-syndrome-r278h-mutation-impairs-b-lymphopoiesis-via-error-prone-nonhomologous-end-joining
#18
Jihye Park, Robert S Welner, Mei-Yee Chan, Logan Troppito, Philipp B Staber, Daniel G Tenen, Catherine T Yan
Hypomorphic mutations in the nonhomologous end-joining (NHEJ) DNA repair protein DNA ligase IV (LIG4) lead to immunodeficiency with varying severity. In this study, using a murine knock-in model, we investigated the mechanisms underlying abnormalities in class switch recombination (CSR) associated with the human homozygous Lig4 R278H mutation. Previously, we found that despite the near absence of Lig4 end-ligation activity and severely reduced mature B cell numbers, Lig4(R278H/R278H) (Lig4(R/R)) mice exhibit only a partial CSR block, producing near normal IgG1 and IgE but substantially reduced IgG3, IgG2b, and IgA serum levels...
January 1, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/26373676/myc-ig-rearrangements-are-negative-predictors-of-survival-in-dlbcl-patients-treated-with-immunochemotherapy-a-gela-lysa-study
#19
RANDOMIZED CONTROLLED TRIAL
Christiane Copie-Bergman, Peggy Cuillière-Dartigues, Maryse Baia, Josette Briere, Richard Delarue, Danielle Canioni, Gilles Salles, Marie Parrens, Karim Belhadj, Bettina Fabiani, Christian Recher, Tony Petrella, Nicolas Ketterer, Frederic Peyrade, Corinne Haioun, Inga Nagel, Reiner Siebert, Fabrice Jardin, Karen Leroy, Jean-Philippe Jais, Herve Tilly, Thierry Jo Molina, Philippe Gaulard
Diffuse large B-cell lymphoma (DLBCL) with MYC rearrangement (MYC-R) carries an unfavorable outcome. We explored the prognostic value of the MYC translocation partner gene in a series of MYC-R de novo DLBCL patients enrolled in first-line prospective clinical trials (Groupe d'Etudes des Lymphomes de l'Adulte/Lymphoma Study Association) and treated with rituximab-anthracycline-based chemotherapy. A total of 774 DLBCL cases characterized for cell of origin by the Hans classifier were analyzed using fluorescence in situ hybridization with BCL2, BCL6, MYC, immunoglobulin (IG)K, and IGL break-apart and IGH/MYC, IGK/MYC, and IGL/MYC fusion probes...
November 26, 2015: Blood
https://www.readbyqxmd.com/read/26364572/immunoglobulin-gene-expression-in-umbilical-cord-blood-derived-cd34%C3%A2-%C2%BA-hematopoietic-stem-progenitor-cells
#20
Jingfang Liu, Miaoran Xia, Pingzhang Wang, Chong Wang, Zihan Geng, C Cameron Yin, Chi Zhang, Xiaoyan Qiu
Recently, immunoglobulin (Ig) expression was reported in a variety of non-B lineage cells, including myeloid cells. We assessed whether hematopoietic stem/progenitor cells (HSC/HPCs) can express Ig. With Gene Expression Omnibus (GEO) microarray database analysis, we found that IGHM was expressed with the highest frequency and level in umbilical cord blood CD34(+) HSC/HPCs, followed by IGK@, IGHE, IGHD, IGHG1, and IGHA1, while IGL@ was nearly not expressed. Ig expression was further confirmed by molecular experiments and immunofluorescence...
January 1, 2016: Gene
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