Altered gene expression upon BCR cross-linking in Burkitt's lymphoma B cell line

Non-circadian aspects of BHLHE40 cellular function in cancer

While many genes specifically act as oncogenes or tumor suppressors, others are tumor promoters or suppressors in a context-dependent manner. Here we will review the basic-helix-loop-helix (BHLH) protein BHLHE40, (also known as BHLHB2, STRA13, DEC1, or SHARP2) which is overexpressed in gastric, breast, and brain tumors; and downregulated in colorectal, esophageal, pancreatic and lung cancer. As a transcription factor, BHLHE40 is expressed in the nucleus, where it binds to target gene promoters containing the E-box hexanucleotide sequence, but can also be expressed in the cytoplasm, where it stabilizes cyclin E, preventing cyclin E-mediated DNA replication and cell cycle progression. In different organs BHLHE40 regulates different targets; hence may have different impacts on tumorigenesis. BHLHE40 promotes PI3K/Akt/mTOR activation in breast cancer, activating tumor progression, but suppresses STAT1 expression in clear cell carcinoma, triggering tumor suppression. Target specificity likely depends on cooperation with other transcription factors. BHLHE40 is activated in lung and esophageal carcinoma by the tumor suppressor p53 inducing senescence and suppressing tumor growth, but is also activated under hypoxic conditions by HIF-1α in gastric cancer and hepatocellular carcinomas, stimulating tumor progression. Thus, BHLHE40 is a multi-functional protein that mediates the promotion or suppression of cancer in a context dependent manner.

Role of CD47 and Signal Regulatory Protein Alpha (SIRPα) in Regulating the Clearance of Viable or Aged Blood Cells

SUMMARY

The ubiquitously expressed cell surface glycoprotein CD47 is expressed by virtually all cells in the host, where it can function to regulate integrin-mediated responses, or constitute an important part of the erythrocyte band 3/Rh multi-protein complex. In addition, CD47 can protect viable cells from being phagocytosed by macrophages or dendritic cells. The latter mechanism is dependent on the interaction between target cell CD47 and SIRPα on the phagocyte. In this context, SIRPα functions to inhibit prophagocytic signaling from Fcγ receptors, complement receptors, and LDL receptor-related protein-1 (LRP-1), but not scavenger receptors. The expression level and/or distribution of CD47 may be altered on the surface of apoptotic/senescent cells, rendering the phagocytosis inhibitory function of the CD47/SIRPα interaction reduced or eliminated. Instead, the interaction between these 2 proteins may serve to enhance the binding of apoptotic/senescent target cells to the phagocyte to promote phagocytosis.

Lineage specificity of gene expression patterns

The hematopoietic system offers many advantages as a model for understanding general aspects of lineage choice and specification. Using oligonucleotide microarrays, we compared gene expression patterns of multiple purified hematopoietic cell populations, including neutrophils, monocytes, macrophages, resting, centrocytic, and centroblastic B lymphocytes, dendritic cells, and hematopoietic stem cells. Some of these cells were studied under both resting and stimulated conditions. We studied the collective behavior of subsets of genes derived from the Biocarta database of functional pathways, hand-tuned groupings of genes into broad functional categories based on the Gene Ontology database, and the metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes database. Principal component analysis revealed strikingly pervasive differences in relative levels of gene expression among cell lineages that involve most of the subsets examined. These results indicate that many processes in these cells behave differently in different lineages. Much of the variation among lineages was captured by the first few principal components. Principal components biplots were found to provide a convenient visual display of the contributions of the various genes within the subsets in lineage discrimination. Moreover, by applying tree-constructing methodologies borrowed from phylogenetics to the expression data from differentiated cells and stem cells, we reconstructed a tree of relationships that resembled the established hematopoietic program of lineage development. Thus, the mRNA expression data implicitly contained information about developmental relationships among cell types.

Expression and activation of signal regulatory protein alpha on astrocytomas

High-grade astrocytomas and glioblastomas are usually unresectable because they extensively invade surrounding brain tissue. Here, we report the expression and function of a receptor on many astrocytomas that may alter both the proliferative and invasive potential of these tumors. Signal regulatory protein (SIRP) alpha1 is an immunoglobulin superfamily transmembrane glycoprotein that is normally expressed in subsets of myeloid and neuronal cells. Transfection of many cell types with SIRPalpha1, including glioblastomas, has been shown to inhibit their proliferation in response to a range of growth factors. Furthermore, the expression of a murine SIRPalpha1 mutant has been shown to enhance cell adhesion and initial cell spreading but to inhibit cell extension and movement. The extracellular portion of SIRPalpha1 binds CD47 (integrin-associated protein), although this interaction is not required for integrin-mediated activation of SIRPalpha1. On phosphorylation, SIRPalpha1 recruits the tyrosine phosphatases SHP-1 and SHP-2, which are important in its functions. Although SHP-1 is uniquely expressed on hematopoietic cells, SHP-2 is ubiquitously expressed, so that SIRPalpha1 has the potential to function in many cell types, including astrocytomas. Because SIRPalpha1 regulates cell functions that may contribute to the malignancy of these tumors, we examined the expression of SIRPs in astrocytoma cell lines by flow cytometry using a monoclonal antibody against all SIRPs. Screening of nine cell lines revealed clear cell surface expression of SIRPs on five cell lines, whereas Northern blotting for SIRPalpha transcripts showed mRNA present in eight of nine cell lines. All nine cell lines expressed the ligand for SIRPalpha1, CD47. To further examine the expression and function of SIRPs, we studied the SF126 and U373MG astrocytoma cell lines, both of which express SIRPs, in greater detail. SIRP transcripts in these cells are identical in sequence to SIRPalpha1. The expressed deglycosylated protein is the same size as SIRPalpha1, but in the astrocytoma cells, it is underglycosylated compared with SIRPalpha1 produced in transfected Chinese hamster ovary cells. It is nonetheless still capable of binding soluble CD47. Moreover, SIRPalpha1 in each of the two cell lines recruited SHP-2 on phosphorylation, and SIRPalpha1 phosphorylation in cultured cells is CD47 dependent. Finally, examination of frozen sections from 10 primary brain tumor biopsies by immunohistochemistry revealed expression of SIRPs on seven of the specimens, some of which expressed high levels of SIRPs. Most of the tumors also expressed CD47. This is the first demonstration that astrocytomas can express SIRPalpha. Given the known role of SIRPalpha in regulating cell adhesion and responses to mitogenic growth factors, the expression of SIRPalpha1 on astrocytomas may be of considerable importance in brain tumor biology, and it offers the potential of a new avenue for therapeutic intervention.

Downregulation of genes involved in DNA repair and differential expression of transcription regulators and phosphatases precede IgM-induced apoptosis in the Burkitt's lymphoma cell line BL60-2

Apoptosis of lymphocytes recognizing self-antigens is an essential mechanism to protect the organism against autoimmune diseases. Programmed cell death of susceptible B cells occurs in response to surface IgM cross-linking mediated by self-antigens. This effect can be mimicked in the Burkitt's lymphoma line BL60-2 by addition of anti-IgM antibodies. In order to identify genes with differential expression in response to the apoptotic stimulus, total RNA prepared from BL60-2 cells before and at different points in time after IgM cross-linking was used for Atlas arrays, high-density oligonucleotide microarrays (GeneChip arrays, Affymetrix) and in RNase protection assays (RPA). One of our major observations was the downregulation of six genes involved in the ligation of DNA strand breaks, like DNA ligases and DNA-PK, indicating a shutdown of DNA repair mechanisms in apoptotic cells. In addition, we found changes on mRNA level for several transcription regulators, including early growth response genes 1 and 2, TAFII30 and topoisomerase I. Furthermore, we show accumulation of mRNA for the phosphatases CD45 and DUSP5 in anti-IgM stimulated BL60-2 cells. Our data provide a basis for further analysis of the differentially expressed genes and their roles in IgM-induced B cell death as well as in apoptosis in other cellular systems.

Expression of myeloid-specific genes in childhood acute lymphoblastic leukemia - a cDNA array study

Several specific cytogenetic changes are known to be associated with childhood acute lymphoblastic leukemia (ALL), and many of them are important prognostic factors for the disease. Little is known, however, about the changes in gene expression in ALL. Recently, the development of cDNA array technology has enabled the study of expression of hundreds to thousands of genes in a single experiment. We used the cDNA array method to study the gene expression profiles of 17 children with precursor-B ALL. Normal B cells from adenoids were used as reference material. We discuss the 25 genes that were most over-expressed compared to the reference. These included four genes that are normally expressed only in the myeloid lineages of the hematopoietic cells: RNASE2, GCSFR, PRTN3 and CLC. We also detected over-expression of S100A12, expressed in nerve cells but also in myeloid cells. In addition to the myeloid-specific genes, other over-expressed genes included AML1, LCP2 and FGF6. In conclusion, our study revealed novel information about gene expression in childhood ALL. The data obtained may contribute to further studies of the pathogenesis and prognosis of childhood ALL.

BXMAS1 identifies a cluster of homologous genes differentially expressed in B cells

Characterization of genes activated by anti-IgM crosslinking of BL2 cells identified one gene, designated BXMAS1, that is predicted to be a novel cell surface receptor. The time course of activation indicates maximal transcriptional induction after 24 h. The predicted protein contains 977 aa residues, with a cytoplasmic domain containing 2 ITIM motifs. The ectodomain of the protein contains 6 repeats of characteristic 93 aa sequences which we have designated BXMAS1 domains. These domains correspond to 6 out of 8 Ig-like domains in BXMAS1. A search of the human genome revealed 5 additional closely linked homologous genes many of which contain BXMAS1 domains as well. Analysis of expression in cell lines and tissues suggests a general restriction of expression of these genes to B cells. These genes may be involved in B cell development and differentiation in peripheral lymphoid organs and may be useful markers of B cell stages.