Stimulation-induced gene expression in Ramos B-cells.

The development of adaptive immunity and responses to foreign molecules and organisms relies on the highly regulated production of hundreds of proteins. B-cell maturation, from committed progenitors to terminally differentiated plasma cells, is a multistep process that requires the ordered expression of a large number of genes. We studied anti-IgM-stimulated Ramos cells to explore genome-wide expression patterns in differentiating human B-cells. cDNA microarrays were used to measure changes in transcript levels over several days. A large set of genes ( approximately 1,500) showed significantly altered expression at one or more time points. The expression profiles were used to construct gene clusters that were then characterized further with respect to the functions of the encoded proteins. Several groups of genes relevant to B-cells were analyzed in detail including early response genes and genes related to transcription, apoptosis and cell cycle regulation. Extensive bioinformatics analyses were conducted to identify the genes/proteins and to study functions and pathways involving B-cells. The results pave the way for understanding the development of humoral immunity, and provide new candidate genes and targets for research and drug development.

Distinct gene expression profiling in chronic lymphocytic leukemia with 11q23 deletion.

Chronic lymphocytic leukemia (CLL) is a heterogeneous disease with regard to its clinical course. The limitations of the methods currently available for prognostic assessment in CLL do not allow accurate prediction of the risk of disease progression in individual patients. The recently developed cDNA array technique provides a unique opportunity to study gene expression in various malignancies. To identify new molecular markers for prognostication of CLL patients, we analyzed cDNA arrays by using hierarchical clustering and standard statistic t-test on 34 CLL patients. We found significant expression differences in 78 genes compared to the reference tonsillar B lymphocytes. A cluster of genes, LCP1, PARP, BLR1, DEK, NPM, MCL1, SLP76, STAM, HIVEP1, EVI2B, CD25, HTLF, HIVEP2, BCL2, MNDA, PBX3, EB12, TCF1, CGRP, CD14, ILB, GZMK, GPR17 and CD79B, was associated (P < 0.05) with the unfavorable 11q deletion and also with the unfavorable Binet stages B and C. We present here gene expression profiling that is associated with CLL patients with the 11q23 deletion. Many of the genes in the cluster have not previously been shown to be related to the initiation or progression of CLL. These novel findings provide fundamental information for further attempts to understand the interaction of the clustered genes in the leukomogenesis of CLL in order to better design treatments aimed at specific molecular target(s).

Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family.

We have isolated the DNMT3L gene that is related to the cytosine-5-methyltransferase 3 (DNMT3) family. The gene is located on chromosome 21q22.3 between the AIRE and the KIAA0653 genes and spans approximately 16 kb of genomic sequence. The encoded protein of 387 amino acids has a cysteine-rich region containing a novel-type zinc finger domain that is conserved in DNMT3A and DNMT3B but also in ATRX, a member of the SNF2 protein family. The novel domain, called an ADD (ATRX, DNMT3, DNMT3L)-type zinc finger, contains two subparts: a C2C2 and an imperfect PHD zinc finger. Expression of the DNMT3L mRNA was not detectable by Northern blotting; however, RT-PCR amplification revealed that it is expressed at low levels in several tissues including testis, ovary, and thymus.

The autoimmune regulator protein has transcriptional transactivating properties and interacts with the common coactivator CREB-binding protein.

Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy, caused by mutations in the autoimmune regulator (AIRE) gene, is an autosomal recessive autoimmune disease characterized by the breakdown of tolerance to organ-specific antigens. The 545 amino acid protein encoded by AIRE contains several structural motifs suggestive of a transcriptional regulator and bears similarity to cellular proteins involved in transcriptional control. We show here that AIRE fused to a heterologous DNA binding domain activates transcription from a reporter promoter, and the activation seen requires the full-length protein or more than one activation domain. At the structural level AIRE forms homodimers through the NH(2)-terminal domain, and molecular modeling for this domain suggests a four-helix bundle structure. In agreement, we show that the common transcriptional coactivator CREB-binding protein (CBP) interacts with AIRE in vitro and in yeast nuclei through the CH1 and CH3 conserved domains. We suggest that the transcriptional transactivation properties of AIRE together with its interaction with CBP might be important in its function as disease-causing mutations almost totally abolish the activation effect.

Stimulation of B and T cells activates expression of transcription and differentiation factors.

During B and T cell differentiation and proliferation many genes are induced or repressed while certain genes are constitutively expressed. To investigate processes related to B and T cell activation, the gene expression of stimulated and nonstimulated Ramos and Jurkat cells was studied using cDNA microarray technology. Simultaneous analysis of close to 600 genes indicated highest increase in the expression of certain transcription, differentiation and proliferation factors. Many of these genes have not previously been shown to funcion in the stimulated lymphocytes. Also genes encoding proteins involved in DNA replication, binding, transcription and translation were induced. Large part of the activated genes were under very stringent regulation being expressed only after stimulation. The mechanism and function of the expressed genes during lymphocyte differentiation and in disorders is discussed.

BTKbase, mutation database for X-linked agammaglobulinemia (XLA).

X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 463 mutation entries from 406 unrelated families showing 303 unique molecular events. In addition to mutations, the database also lists variants or polymorphisms. Each patient is given a unique patient identity number (PIN). Information is included regarding the phenotype including symptoms. Mutations in all the five domains of BTK have been noticed to cause the disease, the most common event being missense mutations. The mutations appear almost uniformly throughout the molecule and frequently affect CpG sites that code for arginine residues. The putative structural implications of all the missense mutations are given in the database. The improved version of the registry having a number of new features is available at http://www. helsinki.fi/science/signal/btkbase.html

Registries of immunodeficiency patients and mutations.

Immunodeficiencies form a distinct group of human hereditary diseases with several rare disorders. During recent years, information has been collected concerning immunodeficiency patients and mutations causing disorders. The large European (ESID) registry contains clinical data for some 7,000 patients. At present, international mutation databases have information for > 1,000 immunodeficiency patients, including X-linked chronic granulomatous disease (XCGD), Wiskott-Aldrich syndrome (WAS), and X-linked thrombocytopenia (XLT), X-linked hyper-IgM syndrome (XHIM), X-linked agammaglobulinemia (XLA), and X-linked severe combined immunodeficiency (XSCID). The databases are available on Internet. The mutation spectra of patients in these registries were compared. Mutational hotspots were found in CpG dinucleotides with a preference for selected flanking bases.

BTKbase, mutation database for X-linked agammaglobulinemia (XLA)

X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 368 entries from 318 unrelated families showing 228 unique molecular events. In addition to mutations the database lists also some polymorphisms and site-directed mutations. Each patient is given a unique patient identity number (PIN). Information is provided regarding the phenotype including symptoms. Mutations in all the five domains of BTK have been noticed to cause the disease, the most common event being missense mutations. The mutations appear almost uniformly throughout the molecule and frequently affect CpG sites forming arginine residues. These hot spots have generally pyrimidines 5'and purines 3'to the mutated cytosine. A decreased frequency of missense mutations was found in the TH, SH3 and the upper lobe of the kinase domain. The putative structural implications of all the missense mutations are given in the database showing 228 unique molecular events, including a novel missense mutation causing an R28C substitution as previously seen in the Xid mouse.

Sequence specificity in CpG mutation hotspots.

CpG dinucleotides are efficiently methylated in vertebrate genomes except in the CpG islands having a high C+G content. Methylated CpGs are the single most mutated dinucleotide. Sequences surrounding disease causing CpG mutation sites were analyzed from locus-specific mutation databases. Both tetra- and heptanucleotide analyses indicated clear overall sequence preference for having pyrimidines 5' and purines 3' to the mutated 5-methylcytosine. The most mutated tetranucleotides are TCGA and TCGG, the former being also a frequent restriction and modification site. The results will help in elucidating the still controversial mutation mechanism of CpG doublets.

Driving ability in cancer patients receiving long-term morphine analgesia.

When given in single doses to healthy volunteers, opioid analgesics impair reaction time, muscle coordination, attention, and short-term memory sufficiently to affect driving and other skilled activities. Despite the increasing use of oral morphine daily, little is known about the effect of long-term opioid therapy on psychomotor performance. To examine the effects of continuous morphine medication, psychological and neurological tests originally designed for professional motor vehicle drivers were conducted in two groups of cancer patients who were similar apart from experience of pain. 24 were on continuous morphine (mean 209 mg oral morphine daily) for cancer pain; and 25 were pain-free without regular analgesics. Though the results were a little worse in the patients taking morphine, there were no significant differences between the groups in intelligence, vigilance, concentration, fluency of motor reactions, or division of attention. Of the neural function tests, reaction times (auditory, visual, associative), thermal discrimination, and body sway with eyes open were similar in the two groups; only balancing ability with closed eyes was worse in the morphine group. These results indicate that, in cancer patients receiving long-term morphine treatment with stable doses, morphine has only a slight and selective effect on functions related to driving.