Cloning and functional characterization of early B-cell factor, a regulator of lymphocyte-specific gene expression.

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by complex interplay among immune cell types. SLE activity is experimentally assessed by several blood tests, including gene expression profiling of heterogeneous populations of cells in peripheral blood. To better understand the contribution of different cell types in SLE pathogenesis, we applied the two methods in cell-type-specific differential expression analysis, csSAM and DSection, to identify cell-type-specific gene expression differences in heterogeneous gene expression measures obtained using RNA-seq technology. We identified B-cell-, monocyte-, and neutrophil-specific gene expression differences. Immunoglobulin-coding gene expression was altered in B-cells, while a ribosomal signature was prominent in monocytes. On the contrary, genes differentially expressed in the heterogeneous mixture of cells did not show any functional enrichment. Our results identify antigen binding and structural constituents of ribosomes as functions altered by B-cell- and monocyte-specific gene expression differences, respectively. Finally, these results position both csSAM and DSection methods as viable techniques for cell-type-specific differential expression analysis, which may help uncover pathogenic, cell-type-specific processes in SLE.

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Characterization of differentiation specific gene expression in embryonic stem cells under serum-reduced culture conditions in the EST

Reproductive Toxicology ◽

10.1016/j.reprotox.2008.05.016 ◽

2008 ◽

Vol 26 (1) ◽

pp. 61-62

Author(s):

Burkhard Flick ◽

Friedericke Rolle ◽

Patrick Scholz ◽

Marcus Wehland ◽

Stephan Klug

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Embryonic Stem Cells ◽

Embryonic Stem ◽

Culture Conditions ◽

Specific Gene ◽

Specific Gene Expression

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Functional analysis of the endothelial cell-specific Tie2/Tek promoter identifies unique protein-binding elements

Biochemical Journal ◽

10.1042/bj3300335 ◽

1998 ◽

Vol 330 (1) ◽

pp. 335-343 ◽

Cited By ~ 18

Author(s):

M. Bahaa FADEL ◽

C. Stephane BOUTET ◽

Thomas QUERTERMOUS

Keyword(s):

Gene Expression ◽

Endothelial Cell ◽

Dna Binding ◽

Protein Binding ◽

Dna Sequences ◽

Molecular Basis ◽

Proximal Promoter ◽

Specific Gene ◽

Specific Gene Expression

To investigate the molecular basis of endothelial cell-specific gene expression, we have examined the DNA sequences and the cognate DNA-binding proteins that mediate transcription of the murine tie2/tek gene. Reporter transfection experiments conformed with earlier findings in transgenic mice, indicating that the upstream promoter of Tie2/Tek is capable of activating transcription in an endothelial cell-specific fashion. These experiments have also allowed the identification of a single upstream inhibitory region (region I) and two positive regulatory regions (regions U and A) in the proximal promoter. Electrophoretic mobility-shift assays have allowed further characterization of three novel DNA-binding sequences associated with these regions and have provided preliminary characterization of the protein factors binding to these elements. Two of the elements (U and A) confer increased transcription on a heterologous promoter, with element U functioning in an endothelial-cell-selective manner. By employing embryonic endothelial-like yolk sac cells in parallel with adult-derived endothelial cells, we have identified differences in functional activity and protein binding that may reflect mechanisms for specifying developmental regulation of tie2/tek expression. Further study of the DNA and protein elements characterized in these experiments is likely to provide new insight into the molecular basis of developmental- and cell-specific gene expression in the endothelium.

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Uniform Expression of Notch1, Suppressor of B-Cell–Specific Gene Expression, in Plasmablastic Lymphoma

Archives of Pathology & Laboratory Medicine ◽

10.5858/2009-0691-oa.1 ◽

2011 ◽

Vol 135 (6) ◽

pp. 770-775

Author(s):

Adam C. Seegmiller ◽

Huan-You Wang ◽

Christa Hladik ◽

Weina Chen

Keyword(s):

Gene Expression ◽

B Cell ◽

Plasma Cell ◽

Primary Effusion Lymphoma ◽

Mtor Pathway ◽

Plasmablastic Lymphoma ◽

Cell Phenotype ◽

Specific Gene ◽

Plasma Cell Myeloma ◽

Specific Gene Expression

Abstract Context.—Although the loss of B-lineage–specific gene expression is a distinctive feature of plasmablastic lymphoma, the underlying mechanism remains poorly understood. A candidate for this mechanism is Notch1 signaling, which interferes with the activity of B-cell–specific transcription factors E2A and early B-cell factor and positively regulates the mammalian target of rapamycin (mTOR) pathway. Objective.—To explore the mechanism of loss of B-cell phenotype by correlating expression of B-cell markers with that of Notch1 and downstream targets of the mTOR pathway in plasmablastic lymphoma. Design.—A combination of flow cytometric and immunohistochemical immunophenotyping techniques was used on 9 cases of plasmablastic lymphoma to correlate loss of B-cell markers with expression of Notch1 and downstream activation of the mTOR pathway. These results are compared with 5 cases of primary effusion lymphoma and 21 cases of plasma cell myeloma. Results.—Plasmablastic lymphoma cases exhibit nearly complete loss of B-cell–associated markers and uniform expression of Notch1, with a predominantly nuclear staining pattern. There is a concurrent activation of the mTOR pathway, indicated by expression of mTOR targets eukaryotic initiation factor 4E–binding protein 1 and phosphorylated ribosomal protein S6 in most cases. Similar results are seen in cases of primary effusion lymphoma and plasma cell myeloma. Conclusions.—These findings suggest that activation of Notch1 may be involved in suppression of B-cell–specific gene expression and global loss of the B-cell phenotype in plasmablastic lymphoma, similar to primary effusion lymphoma and plasma cell myeloma. Thus, there might be a role for the Notch1 and mTOR pathways in the pathogenesis and therapy of plasmablastic lymphoma.

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