Reduced expression of innate immunity-related genes in lymph node metastases of luminal breast cancer patients

Immune system plays a dual role in cancer by either targeting or supporting neoplastic cells at various stages of disease, including metastasis. Yet, the exact immune-related transcriptome profiles of primary tumours (PT) and lymph node metastases (LNM) and their evolution during luminal breast cancer (BCa) dissemination remain undiscovered. In order to identify the immune-related transcriptome changes that accompany lymphatic spread, we analysed PT-LNM pairs of luminal BCa using NanoString technology. Decrease in complement C3-one of the top-downregulated genes, in LNM was validated at the protein level using immunohistochemistry. Thirty-three of 360 analysed genes were downregulated (9%), whereas only 3 (0.8%) upregulated in LNM when compared to the corresponding PT. In LNM, reduced expression was observed in genes related to innate immunity, particularly to the complement system (C1QB, C1S, C1R, C4B, CFB, C3, SERPING1 and C3AR1). In validation cohort, complement C3 protein was less frequently expressed in LNM than in PT and it was associated with worse prognosis. To conclude, local expression of the complement system components declines during lymphatic spread of non-metastatic luminal BCa, whilst further reduction of tumoral complement C3 in LNM is indicative for poor survival. This points to context-dependent role of complement C3 in BCa dissemination.

Chronic Refractory Immune Thrombocytopenia Is Associated With Variants in Immune Genes

The pathogenesis of chronic refractory immune thrombocytopenia (C/RITP) is mechanistically complex and considerably varies across patients. Few studies have focused on the genetic characteristics of C/RITP in children. The aim of this study was to analyze and summarize the clinical manifestations and genetic characteristics of C/RITP children with mutations in immune-related genes. In the study, 51 children with variants in immune-related genes (mutation group) and 103 children with no abnormal mutations (control group) were enrolled. Children in the mutation group showed severity of hemorrhage, a higher incidence of abnormal immunological indices, and an increased expression of SLE biomarkers. The number of peripheral T and B lymphocytes in the mutation group significantly increased. Nine patients (17.6%) had probable pathogenic variant genes associated with primary immunodeficiencies (TNFRSF13B, CARD11, CBL, and RAG2), and 42 patients (82.4%) had variants of uncertain significance in 23 genes. C/RITP patients with variants in immune-related genes had more severe bleeding, abnormal immunological indices, and an increased expression of SLE biomarker. Next-generation sequenciong (NGS) might be a useful way to differentiate those patients from C/RITP.

Immune-related functions of the Hivep gene family in East African cichlid fishes

Immune-related genes are often characterized by adaptive protein evolution. Selection on immune genes can be particularly strong when hosts encounter novel parasites, for instance, after the colonization of a new habitat or upon the exploitation of vacant ecological niches in an adaptive radiation. We examined a set of new candidate immune genes in East African cichlid fishes. More specifically, we studied the signatures of selection in five paralogs of the human immunodeficiency virus type I enhancer-binding protein (Hivep) gene family, tested their involvement in the immune defense, and related our results to explosive speciation and adaptive radiation events in cichlids. We found signatures of long-term positive selection in four Hivep paralogs and lineage-specific positive selection in Hivep3b in two radiating cichlid lineages. Exposure of the cichlid Astatotilapia burtoni to a vaccination with Vibrio anguillarum bacteria resulted in a positive correlation between immune response parameters and expression levels of three Hivep loci. This work provides the first evidence for a role of Hivep paralogs in teleost immune defense and links the signatures of positive selection to host-pathogen interactions within an adaptive radiation.

Sequence polymorphism and expression variability of Crassostrea gigas immune related genes discriminate two oyster lines contrasted in term of resistance to summer mortalities

Summer mortalities of Crassostreagigas are a major concern in oyster aquaculture. They are the result of a complex interaction between the host, pathogens and environmental factors. Oyster genetics have been identified as an essential determinant of oyster susceptibility to summer mortalities. As the capability of oysters to circumvent diseases depends in part on their immune defenses, we aimed to analyze the gene expression and sequence polymorphism of 42 immune related genes in two oyster lines selected for their “High” (H) and “Low” (L) survival to summer mortalities. Results showed that the variability of gene expression and the sequence polymorphism acting on particular genes could enable the discrimination between H and L oyster lines. Besides, a higher sequence polymorphism was observed on the L line affecting 11 of the 42 analyzed genes. By analyzing gene expression, sequence polymorphism and gene copy number of two antimicrobial peptide families (Cg-Defs and Cg-Prp), and an antimicrobial protein (Cg-BPI) on individual oysters, we showed that gene expression and/or sequence polymorphism could also discriminate H and L oyster lines. Finally, we observed a positive correlation between the gene expression and the gene copy number of antimicrobials and that sequence polymorphism could be encoded in the genome. Overall, this study gives new insights in the relationship between oyster immunity and divergent phenotypes, and discusses the potential implication of antimicrobial diversity in oyster survival to summer mortalities.

Global gene expression analysis of chicken caecal response to Campylobacter jejuni

Campylobacter jejuni colonises the caecum of more than 90% of commercial chickens. Even though colonisation is asymptomatic, we hypothesised that it is mediated by activation of several biological pathways. We therefore used chicken-specific 20K oligonucleotide microarrays to examine global gene expression in C. jejuni-challenged birds. Microarray results demonstrate small but significant fold-changes in expression of 270 genes 20 h post-challenge, corresponding to a wide range of biological processes including cell growth, nutrient metabolism and immunological activity. Expression of NOX1 (2.3-fold) and VCAM1 (1.5-fold) were significantly increased in colonised birds (P<0.05), indicating oxidative burst and endothelial cell activation, respectively. Microarray results, supplemented by qRT-PCR analyses demonstrated increased TOPK (1.9-fold), IL17 (3.6-fold), IL21 (2.1-fold), IL7R (4-fold) and CTLA4 (2.5-fold) gene expression (P<0.05), which was suggestive of T cell mediated activity. Combined these results suggest that C. jejuni has nominal effects on global caecal gene expression in the chicken but significant changes detected are suggestive of a protective intestinal T cell response.

Induction of interferon-stimulated genes by Chlamydia pneumoniae in fibroblasts is mediated by intracellular nucleotide-sensing receptors

Background

Recognition of microorganisms by the innate immune system is mediated by pattern recognition receptors, including Toll-like receptors and cytoplasmic RIG-I-like receptors. Chlamydia, which include several human pathogenic species, are obligate intracellular gram-negative bacteria that replicate in cytoplasmic vacuoles. The infection triggers a host response contributing to both bacterial clearance and tissue damage. For instance, type I interferons (IFN)s have been demonstrated to exacerbate the course of Chlamydial lung infections in mice.

Methods/Principal Findings

Here we show that Chlamydia pneumoniae induces expression of IFN-stimulated genes (ISG)s dependent on recognition by nucleotide-sensing Toll-like receptors and RIG-I-like receptors, localized in endosomes and the cytoplasm, respectively. The ISG response was induced with a delayed kinetics, compared to virus infections, and was dependent on bacterial replication and the bacterial type III secretion system (T3SS).

Conclusions/Significance

Activation of the IFN response during C. pneumoniae infection is mediated by intracellular nucleotide-sensing PRRs, which operate through a mechanism dependent on the bacterial T3SS. Strategies to inhibit the chlamydial T3SS may be used to limit the detrimental effects of the type I IFN system in the host response to Chlamydia infection.

Expression of immune-related genes in one phase of embryonic development of freshwater crayfish, Pacifastacus leniusculus

Crayfish do not have larval stage as other crustacean such as penaeid shrimp they spawn their eggs until hatching and what hatches out from the eggs are miniature crayfish known as juveniles. In order to address the question whether immune genes are initially expressed during the embryo development in the egg stage, the expression of some immune-related genes: prophenoloxidase (proPO), peroxinectin, hemocyanin, anti-lipopolysaccharide factor (ALF), plcrustin, astakine-1, 2 and transglutaminase (TGase) were determined in the middle phase of crayfish embryo development. Furthermore, immune challenge was used to determine the immune response of eggs by immersing them in a solution of the highly pathogenic bacterium Aeromonas hydrophila. Semi-quantitative RT-PCR analysis showed that all tested genes are present except proPO in this phase of crayfish embryo development and none of the genes tested changed their expression following immersion in A. hydrophila. The proPO transcript has been reported from hemocytes in crustaceans and it plays crucial roles in crustacean immune response. This may indicate that the development of immune-competent hemocytes in this stage of crayfish embryo is not completed and the egg shell as such plays an important role as a shield in protecting the embryo from bacteria and maybe also other pathogens.

Immune responses and expression profiles of some immune-related genes in Indian major carp, Labeo rohita to Edwardsiella tarda infection

Edwardsiella tarda is an important Gram-negative bacterium that causes systemic infections in a wide range of hosts including fish. The pathogenic mechanisms in this disease are still poorly understood in fish. Indian major carp, Labeo rohita were intraperitoneally challenged with a pathogenic isolate of E. tarda to measure sequential changes in immunity level. A significant decrease in the superoxide production, myeloperoxidase, alternative complement activity, total protein levels and antiprotease activity of serum was marked in the infected fish. However, the serum lysozyme activity and haemagglutination titre were raised in the infected fish. Similarly, a significant rise in specific antibody titre was noticed on and after 10 days post-challenge. This study also elucidates the changes in the relative expression of some immune-related genes viz., interleukin 1-beta (IL-1beta), inducible nitric oxide synthase (iNOS), complement component C3, beta(2)-microglobulin, CXCa, tumor necrosis factor-alpha (TNFalpha), and C-type and G-type lysozymes during the infection. Significant up-regulation of IL-1beta, iNOS, C3, CXCa and expression of both types of lysozyme genes was noticed at 6-12 h post-challenge (h.p.c.) whereas down-regulation of beta(2)-microglobulin and TNFalpha genes was observed after 48 h p.c. The results obtained here strengthen the understanding on molecular pathogenesis of edwardsiellosis in L. rohita.

Prediction of antibody response using recombinant human protein fragments as antigen

A great need exists for prediction of antibody response for the generation of antibodies toward protein targets. Earlier studies have suggested that prediction methods based on hydrophilicity propensity scale, in which the degree of exposure of the amino acid in an aqueous solvent is calculated, has limited value. Here, we show a comparative analysis based on 12,634 affinity-purified antibodies generated in a standardized manner against human recombinant protein fragments. The antibody response (yield) was measured and compared to theoretical predictions based on a large number (544) of published propensity scales. The results show that some of the scales have predictive power, although the overall Pearson correlation coefficient is relatively low (0.2) even for the best performing amino acid indices. Based on the current data set, a new propensity scale was calculated with a Pearson correlation coefficient of 0.25. The values correlated in some extent to earlier scales, including large penalty for hydrophobic and cysteine residues and high positive contribution from acidic residues, but with relatively low positive contribution from basic residues. The fraction of immunogens generating low antibody responses was reduced from 30% to around 10% if immunogens with a high propensity score (>0.48) were selected as compared to immunogens with lower scores (<0.29). The study demonstrates that a propensity scale might be useful for prediction of antibody response generated by immunization of recombinant protein fragments. The data set presented here can be used for further studies to design new prediction tools for the generation of antibodies to specific protein targets.

Identification of immune-related genes from kidney and spleen of turbot, Psetta maxima (L.), by suppression subtractive hybridization following challenge with Vibrio harveyi

Suppression subtractive hybridization was used to investigate the response of turbot, Psetta maxima (L.), to Vibrio harveyi, by using a cDNA library constructed from artificially infected turbot kidney and spleen mRNA. Forty-nine expressed sequence tags were obtained. Several immune system genes were identified, including a major histocompatibility complex (MHC) class Ia gene and a heat shock protein 70 gene. Some signalling molecules were also present in the cDNA libraries, including src-family tyrosine kinase SCK, sgk-1 serine-threonine protein kinase and amyloid precursor-like protein 2. The full length of MHC class Ia cDNA was cloned from turbot cDNA by rapid amplification of cDNA ends polymerase chain reaction. The nucleotide sequence of turbot MHC class Ia has been submitted to GenBank with accession number EF032639. The turbot MHC class Ia cDNA has an open reading frame encoding 354 amino acids, and the deduced amino acid sequence of turbot MHC class Ia has 68%, 54%, 51%, 52%, 57%, 33%, 29% and 29% identities to those of olive flounder, medaka, rainbow trout, Atlantic cod, tiger puffer, chicken, mouse and human, respectively. Quantitative reverse transcriptase-PCR was performed for the MHC class Ia gene, and it was revealed that the expression level of the MHC class Ia gene in V. harveyi-challenged turbot increased to fourfold that of the controls.

Immune-related gene expression profiling of yellowtail (Seriola quinqueradiata) kidney cells stimulated with ConA and LPS using microarray analysis

To better understand the immune system of a commercially important fish (yellowtail, Seriola quinqueradiata), we constructed a cDNA microarray containing 1001 selected genes from yellowtail EST and used this to investigate gene expression of primary cultured kidney cells stimulated with ConA and LPS. The total number of up-regulated genes stimulated by LPS was apparently greater than that of ConA stimulation, whereas down-regulated genes were markedly found in ConA-stimulated group. Of the genes that were up-regulated at 3, 6, and 12h after LPS treatment, 12%, 13% and 12%, respectively, were immune-related. Immune-related genes were sorted into 4 groups based on their differential expression patterns against LPS induction. LPS induced the expression of genes related to inflammation, cytokine activity, antigen presentation and antigen binding such as, IL-1beta, CC chemokine with stalk CK2, MHC class II beta chain and immunoglobulin heavy chain. Amplified fragments of RT-PCR products of IgM, IL-1beta, nephrosin, and beta-actin had signal intensities that were comparable to those obtained with the microarray. Overall, these results show that microarrays are a promising tool for uncovering immune mechanism in teleost fish. cDNA sequences of genes were deposited in the GenBank database at DDBJ with accession numbers BB 996897-BB 997897.

Tissue expressions of nine genes important to immune defence of the Pacific white shrimp Litopenaeus vannamei

The tissue expressions of nine immune related genes in apparently healthy Pacific white shrimp Litopenaeus vannamei were analyzed by conventional RT-PCR, quantitative real time PCR (qPCR) and in situ hybridisation. The nine genes were beta-glucan binding protein-high density lipoprotein (BGBP-HDL), lipopolysaccharide-beta-glucan binding protein (LGBP), haemocyanin, prophenoloxidase (proPO), transglutaminase (TGase), crustins, penaeidins (PEN), cytosolic manganese superoxide dismutase (cMnSOD), and lysozyme. Transcripts of all nine genes were detected in all tissues with differential expression levels when examined by RT-PCR and qPCR. BGBP-HDL, LGBP and haemocyanin were mainly expressed in the hepatopancreas and their expressions levels were about 1/10-1/3 those of beta-actin. Their expressions in other tissues were relatively limited. ProPO, TGase, crustins, PEN-3, and lysozyme showed the highest levels of expression in haemocytes and the lowest in hepatopancreas. Their expression levels in the haemocytes were 3 (PEN-3) to 10(-2) (proPO) times those of beta-actin. In contrast to the other genes, cMnSOD showed higher expression levels in haemolymph related organ, stomach and muscle; and lower expression levels in haemocyte, migut, neural ganglion and hepatopancreas. When examined by in situ hybridisation, hepatopancreatic F cells were found to be the major cell type that produced transcripts of BGBP-HDL, LGBP and haemocyanin. On the other hand, circulatory haemocytes and haemocytes infiltrated in various tissues contributed to the expressions of proPO, TGase, crustins, PEN-3 and lysozyme. Both hepatopancreatic F cell and haemocyte generated cMnSOD transcripts. Using in situ hybridisation, the present study is the first to show the tissue distributions of BGBP-HDL, LGBP, haemocyanin, TGase, crustins and cMnSOD in healthy white shrimp. The present results provide a baseline data of physiological expressions for the genes that are important in immune activation and modulation in Pacific white shrimp and a guideline of tissue or organ sampling for effective gene expression analyses for future immunological studies.

Identifying novel genes contributing to asthma pathogenesis

PURPOSE OF REVIEW

To illustrate recent examples of novel asthma genes such as those encoding G-protein-coupled receptor for asthma susceptibility, filaggrin and tenascin-C, and to describe the process that is needed to translate these findings to the clinic.

RECENT FINDINGS

Many hundreds of studies have been published investigating the association of genetic polymorphisms in candidate genes with asthma. These genes were selected on the basis of the gene's product known involvement in the disease process. Moreover, it is the identification of novel genes through hypothesis-independent approaches such as genome-wide linkage studies that is likely to radically alter our understanding of asthma pathophysiology. The identification of a gene is, however, only the first step in a long process that may eventually lead from gene to treatment. This process includes replication, functional studies and, finally, intervention studies.

SUMMARY

While significant progress has been made in the identification of asthma susceptibility genes, it is clear that issues such as replication and functional characterization mean that considerably more research is required. This may enable us to realize benefits to patient treatment that studies of the genetic basis of asthma have the potential to deliver.

Assignment of immune-related genes to the channel catfish, Ictalurus punctatus, genetic map

Eighteen new genes, adenosine A1 receptor (ADORA1), complement component 4-beta (C4b), complement component 8-beta (C8b), chemokine ligand 19 (CCL19), chemokine ligand 21 (CCL21), chemokine ligand 25 (CCL25), chemokine receptor 2 (CCR2), chemokine receptor 5 (CCR5), chemokine receptor 4 (CCR4), chemokine receptor 7 (CCR7), chemokine receptor 9 (CCR9), interleukin 1-beta (IL1B), integrin II-beta (ITGB2), novel immune type receptor 2 (NITR2), novel immune type receptor 4 (NITR4), natural killer cell lysin (NKLYSIN), nucleotide excision repair (RAD23B) and tumour necrosis factor-alpha (TNF), were assigned to the channel catfish (Ictalurus punctatus) genetic linkage map. Polymorphic microsatellite markers were developed for NITR2, NITR4 and RAD23B from short-tandem repeats in the available sequence. Polymorphic microsatellite markers were developed for the remaining 15 genes by short-tandem repeat-anchored primer sequencing of catfish bacterial artificial chromosomes. Two gene clusters (MYOG-NRAMP-ADORA1) and (CCR4-CCR2-CCR5) displayed conservation of synteny between catfish and mammals. Assignment of 18 new genes to the catfish linkage map will further advance integration of genetic and physical maps and comparative mapping between channel catfish and map rich species.

Cytogenetic mapping of immunity-related genes in the domestic horse

Chromosomal locations of 19 horse immunity-related loci (CASP1, CD14, EIF5A, FCER1A, IFNG, IL12A, IL12B, IL12RB2, IL1A, IL23A, IL4, IL6, MMP7, MS4A2, MYD88, NOS2A, PTGS2, TFRC and TLR2) were determined by fluorescence in situ hybridization. For IFNG and PTGS2, this study is a confirmation of their previously reported position. In addition, microsatellite (HMBr1) was localized in the same region as IFNG. All genes were assigned to regions of conserved synteny and the data obtained in this study enhance the comparative human-horse map. Cytogenetic localization of IL6 to ECA4q14-q21.1 suggested a new breakage point that changes the order of loci compared with HSA7. The map assignments of these loci serve as anchors for other loci and will aid in the search for candidate genes associated with traits in the horse.

Identification of expressed genes in carp (Cyprinus carpio) head kidney cells after in vitro treatment with immunostimulants

We analysed a total of 530 expressed genes from the head kidney cells of common carp (Cyprinus carpio) treated by immunostimulants. Sequences of the cDNA clones were compared with sequences in the GenBank database. Immune-related genes identified after in vitro stimulation of carp head kidney cells were: BPI/LBP, C-type lectins, fucolectins, CC-chemokine, CXC-chemokine, CD18, cyclophilin, FcgammaR, G-CSFR, HSP 70, Ig heavy and light chains, NITR, integrin beta2-alpha, Mx, interleukin-1beta, beta thymosin, lysozyme G & C, MHC class II associated invariant chain 1 and 2, granulin, CAAT binding protein and tumour necrosis factor-alpha induced protein. The expression of these immune-related genes may be important for estimating the efficacy of immunostimulants.

Uterine extracellular matrix components are altered during defective decidualization in interleukin-11 receptor alpha deficient mice

BACKGROUND

Implantation of the embryo and successful pregnancy are dependent on the differentiation of endometrial stromal cells into decidual cells. Female interleukin-11 receptor alpha (IL-11Ralpha) deficient mice are infertile due to disrupted decidualization, suggesting a critical role for IL-11 and its target genes in implantation. The molecular targets of IL-11 in the uterus are unknown, but it is likely that IL-11 signaling modifies the expression of other genes important in decidualization. This study aimed to identify genes regulated by IL-11 during decidualization in mouse uterus, and to examine their expression and localization as an indication of functional significance during early pregnancy.

METHODS

Decidualization was artificially induced in pseudopregnant wild type (IL11Ra+/+) and IL-11Ralpha deficient (IL11Ra-/-) littermates by oil injection into the uterine lumen, and gene expression analyzed by NIA 15K cDNA microarray analysis at subsequent time points. Quantitative real-time RT-PCR was used as an alternative mRNA quantitation method and the expression and cellular localization of the protein products was examined by immunohistochemistry.

RESULTS

Among 15,247 DNA probes, 13 showed increased and 4 decreased expression in IL11Ra-/- uterus at 48 h of decidualization. These included 4 genes encoding extracellular matrix proteins; collagen III alpha1, secreted acidic cysteine-rich glycoprotein (SPARC), biglycan and nidogen-1 (entactin). Immunohistochemistry confirmed increased collagen III and biglycan protein expression in IL11Ra-/- uterus at this time. In both IL11Ra-/- and wild type uterus, collagen III and biglycan were primarily localized to the outer connective tissue and smooth muscle cells of the myometrium, with diffuse staining in the cytoplasm of decidualized stromal cells.

CONCLUSION

These data suggest that IL-11 regulates changes in the uterine extracellular matrix that are necessary for decidualization.

Henry Kunkel, Stephanie Smith, clinical immunology, and split genes

The York Avenue (New York) 'ecosystem' from the 1940s through the 1980s enabled Henry Kunkel to apply new scientific methodology to understanding human disease. Stephanie Smith, a young woman with lupus, was treated at the Rockefeller University Hospital in the 1960s. Studies of her antinuclear antibodies by Kunkel and Eng Tan led to the discovery of a precipitin line specific for lupus, and the responsible antigen was designated Sm (for 'Smith'). This review outlines the history of Sm antigen from an interesting precipitin line to the identification of small nuclear RNA molecules and small nuclear ribonucleoproteins, and subsequently the discovery of RNA splicing. The story illustrates Henry Kunkel's approach to science, emphasizing how 'accidental' clinical observations, in the hands of skilled investigators, can have unexpected and potentially momentous implications.

Microarray analysis identifies interferon beta-regulated genes in multiple sclerosis

The molecular mechanisms for the interferon beta (IFNbeta) treatment of multiple sclerosis (MS) remain to be characterized. Using cDNA microarray technology, we have compared the gene expression profile of T and non-T cells derived from relapsing-remitting MS before and after treatment with IFNbeta-1b. IFNbeta treatment significantly altered expression of 21 genes out of 1263 at 3 and 6 months after treatment. These genes included nine with IFN-responsive promoter elements. Whereas there was no change in Th1 or Th2 marker genes, some of the changes were unexpected but coincided with the beneficial effect of IFNbeta in MS.

Computationally identifying novel NF-kappa B-regulated immune genes in the human genome

Identifying novel NF-kappa B-regulated immune genes in the human genome is important to our understanding of immune mechanisms and immune diseases. We fit logistic regression models to the promoters of 62 known NF-kappa B-regulated immune genes, to find patterns of transcription factor binding in the promoters of genes with known immune function. Using these patterns, we scanned the promoters of additional genes to find matches to the patterns, selected those with NF-kappa B binding sites conserved in the mouse or fly, and then confirmed them as NF-kappa B-regulated immune genes based on expression data. Among 6440 previously identified promoters in the human genome, we found 28 predicted immune gene promoters, 19 of which regulate genes with known function, allowing us to calculate specificity of 93%-100% for the method. We calculated sensitivity of 42% when searching the 62 known immune gene promoters. We found nine novel NF-kappa B-regulated immune genes which are consistent with available SAGE data. Our method of predicting gene function, based on characteristic patterns of transcription factor binding, evolutionary conservation, and expression studies, would be applicable to finding genes with other functions.

B cell developmental requirement for the G alpha i2 gene

Null mutation of the Galphai2 trimeric G protein results in a discrete and profound mucosal disorder, including inflammatory bowel disease (IBD), attenuation of IL-10 expression, and immune function polarized to Th1 activity. Genetic and adoptive transfer experiments have established a role for B cells and IL-10 in mucosal immunologic homeostasis and IBD resistance. In this study, we addressed the hypothesis that Galphai2 is required for the development of IL-10-producing B cells. Galphai2(-/-) mice were reduced in the relative abundance of marginal zone (MZ), transitional type 2 (T2), and B-1a B cells and significantly increased in follicular mature and B-1b B cells. Reconstitution of RAG2(-/-) mice with Galphai2(-/-) bone marrow induced an IBD-like colitis and a deficiency in absolute numbers of MZ, T2, and B-1 B cells. Thus, the Galphai2(-/-) genotype in colitis susceptibility and B cell development involved a cis effect within the hemopoietic compartment. In vitro, the B cell population of Galphai2(-/-) mice was functionally deficient in LPS-induced proliferation and IL-10 production, consistent with the exclusive capacity of T2 and MZ cell subpopulations for LPS responsiveness. In vivo, Galphai2(-/-) mice were selectively impaired for the IgM response to T-independent type II, consistent with the relative depletion of MZ and peritoneal B-1 subpopulations. Collectively, these results reveal a selective role for Galphai2 in MZ and B-1 B cell development. Disorders of this Galphai2-dependent process in B cell development may represent a mechanism for IBD susceptibility.

DNA-containing extracellular 50-nm particles in the ileal Peyer's patch of sheep

Follicles of the ileal Peyer's patch are sites of B cell proliferation and of diversification of the primary immunoglobulin repertoire in ruminants. We demonstrate here that 50-nm carbonic anhydrase-reactive particles released in the intercellular space in the follicle-associated epithelium of the ileal Peyer's patch of lambs contain DNA protected with a detergent-resistant membrane. We named these particles DiCAPs (DNA in carbonic anhydrase particles). DiCAPs can be purified from a suspension collected from ileal Peyer's patch follicles by sedimentation in a sucrose gradient. The DiCAP membrane is resistant to several ionic and non-ionic detergents alone, but can be disrupted by a combination of Triton X-100 and proteinase K. Differential nuclease treatment of purified DiCAPs indicates that they contain DNA. Digestion of DiCAP DNA with six-base pair restriction enzymes produces smears, suggesting that individual DiCAPs contain unique sequences. Nonetheless, the size of DiCAP DNA is smaller (approximately 16 kb) than that of lamb genomic DNA. Polymerase chain reaction and sequence analysis of DiCAP DNA reveals the presence of light and heavy chain variable genes as well as housekeeping genes. The data demonstrate the presence of DNA in these extracellular particles, and suggest a role of DiCAPs in transfer of DNA between cells within the ileal Peyer's patch. This raises the possibility of a novel form of communication between cells mediated by nucleic acids.

The mouse (Mus musculus) T cell receptor delta variable (TRDV), diversity (TRDD) and joining (TRDJ) genes

'The Mouse (Mus musculus) T Cell Receptor Delta Variable (TRDV), Diversity (TRDD) and Joining (TRDJ) Genes', the 15th report of the 'IMGT Locus in Focus' section, comprises 7 tables entitled: (1) 'Number of mouse (Mus musculus) germline TRDV genes at 14D1-D2 and potential repertoire'; (2) 'Mouse (Mus musculus) germline TRDV genes at 14D1-D2'; (3) 'Mouse (Mus musculus) TRDV allele table'; (4) 'Mouse (Mus musculus) germline TRDD genes and alleles'; (5) 'Mouse (Mus musculus) germline TRDJ genes'; (6) 'Mouse (Mus musculus) TRDJ allele table', and (7) 'Correspondence between the different mouse (Mus musculus) TRDV gene nomenclatures'. These tables are available at the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http://imgt.cines. fr:8104) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, Montpellier, France.

Molecular cloning, characterization, and expression of TNF cDNA and gene from Japanese flounder Paralychthys olivaceus

We cloned a cDNA and the gene for Japanese flounder TNF. The TNF cDNA consisted of 1217 bp, which encoded 225 amino acid residues. The identities between Japanese flounder TNF and members of the mammalian TNF family were approximately 20-30%. The positions of cysteine residues that are important for disulfide bonds were conserved with respect to those in mammalian TNF-alpha. The Japanese flounder TNF gene has a length of approximately 2 kbp and consists of four exons and three introns. The positions of the exon-intron junction positions of Japanese flounder TNF gene are similar to those of human TNF-alpha. However, the length of the first intron of Japanese flounder is much shorter than that of the human TNF-alpha gene. There are simple CA or AT dinucleotide repeats in the 5'-upstream and 3'-downstream regions of the Japanese flounder TNF gene. Southern blot hybridization indicted that Japanese flounder TNF exists as a single copy. Expression of Japanese flounder TNF mRNA is greatly induced after stimulation of PBLs with LPS, Con A, or PMA. These results indicated that Japanese flounder TNF is more like mammalian TNF-alpha than mammalian lymphotoxin-alpha, with respect to its gene structure, length of amino acid sequence, number and position of cysteine residues, and regulation of gene expression.

Over-expression of the decoy receptor 3 (DcR3) gene in peripheral blood mononuclear cells (PBMC) derived from silicosis patients

Dysregulation of apoptosis, particularly in the Fas/Fas ligand (FasL) pathway, is considered to be involved in the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE). Recently, a soluble decoy receptor, termed decoy receptor 3 (DcR3), that binds FasL and inhibits FasL-induced apoptosis, has been identified. Silicosis is clinically characterized not only by respiratory disorders but by immunological abnormalities. We have found that serum soluble Fas (sFas) levels are elevated in silicosis patients and that sFas message is dominantly expressed in PBMC derived from these patients. This study examined DcR3 gene expression in PBMC derived from patients with silicosis, SLE, or progressive systemic sclerosis (PSS), and compared it with that in healthy volunteers (HV). The relative expression level of the DcR3 gene was examined in PBMC derived from 37 patients with silicosis without clinical symptoms of autoimmune disease, nine patients with SLE, 12 patients with PSS, and 28 HV using the semiquantitative multiplex-reverse transcriptase-polymerase chain reaction (MP-RT-PCR). The correlation between the relative expression level of the DcR3 gene and multiple clinical parameters for respiratory disorders and immunological abnormalities in individuals with silicosis was analysed. The DcR3 gene was significantly over-expressed in cases of silicosis or SLE when compared with HV. In addition, the DcR3 relative expression level was positively correlated with the serum sFas level in silicosis patients. It is unclear, however, whether over-expression of the DcR3 gene in silicosis is caused by chronic silica exposure, merely accompanies the alteration in Fas-related molecules, or precedes the clinical onset of autoimmune abnormalities. It will be necessary to study these patients further, establish an in vitro model of human T cells exposed recurrently to silica compounds, and resolve whether the increase in DcR3 mRNA expression is a cause or consequence of disease.

The Th1/Th2 balance does not account for the difference of susceptibility of mouse strains to Theiler's virus persistent infection

Theiler's virus causes a persistent infection with demyelination that is studied as a model for multiple sclerosis. Inbred strains of mice differ in their susceptibility to viral persistence due to both H-2 and non-H-2 genes. A locus with a major effect on persistence has been mapped on chromosome 10, close to the Ifng locus, using a cross between susceptible SJL/J and resistant B10.S mice. We now confirm the existence of this locus using two lines of congenic mice bearing the B10.S Ifng locus on an SJL/J background, and we describe a deletion in the promoter of the Ifng gene of the SJL/J mouse. We studied the expression of IFN-gamma, IL-2, IL-10, and IL-12 in the brains of SJL/J mice, B10.S mice, and the two lines of congenic mice during the first 2 wk following inoculation. We found a greater expression of IFN-gamma and IL-2 mRNA in the brains of B10.S mice compared with those of SJL/J mice. Also, the ratio of IL-12 to IL-10 mRNA levels was higher in B10.S mice. However, the cytokine profiles were the same for the two lines of resistant congenic mice and for susceptible SJL/J mice. Therefore, the difference of Th1/Th2 balance between the B10.S and SJL/J mice is not due to the Ifng locus and does not account for the difference of susceptibility of these mice to persistent infection.

Molecular cloning and characterization of a novel CD1 gene from the pig

Much effort is underway to define the immunological functions of the CD1 multigene family, which encodes a separate lineage of Ag presentation molecules capable of presenting lipid and glycolipid Ags. To identify porcine CD1 homologues, a cosmid library was constructed and screened with a degenerate CD1 alpha3 domain probe. One porcine CD1 gene (pCD1.1) was isolated and fully characterized. The pCD1.1 gene is organized similarly to MHC class I and other CD1 genes and contains an open reading frame of 1020 bp encoding 339 amino acids. Expression of pCD1.1 mRNA was observed in CD3- thymocytes, B lymphocytes, and tissue macrophages and dendritic cells. The pCD1.1 cDNA was transfected into Chinese hamster ovary cells, and subsequent FACS analysis demonstrated that mAb 76-7-4, previously suggested to be a pig CD1 mAb, recognizes cell surface pCD1.1. Structurally, the pCD1.1 alpha1 and alpha2 domains are relatively dissimilar to those of other CD1 molecules, whereas the alpha3 domain is conserved. Overall, pCD1.1 bears the highest similarity with human CD1a, and the ectodomain sequences characteristically encode a hydrophobic Ag-binding pocket. Distinct from other CD1 molecules, pCD1.1 contains a putative serine phosphorylation motif similar to that found in human, pig, and mouse MHC class Ia molecules and to that found in rodent, but not human, MHC class-I related (MR1) cytoplasmic tail sequences. Thus, pCD1.1 encodes a molecule with a conventional CD1 ectodomain and an MHC class I-like cytoplasmic tail. The unique features of pCD1.1 provoke intriguing questions about the immunologic functions of CD1 and the evolution of Ag presentation gene families.

Two constituents of the initiation complex of the mannan-binding lectin activation pathway of complement are encoded by a single structural gene

Mannan-binding lectin (MBL) forms a multimolecular complex with at least two MBL-associated serine proteases, MASP-1 and MASP-2. This complex initiates the MBL pathway of complement activation by binding to carbohydrate structures present on bacteria, yeast, and viruses. MASP-1 and MASP-2 are composed of modular structural motifs similar to those of the C1q-associated serine proteases C1r and C1s. Another protein of 19 kDa with the same N-terminal sequence as the 76-kDa MASP-2 protein is consistently detected as part of the MBL/MASP complex. In this study, we present the primary structure of this novel MBL-associated plasma protein of 19 kDa, MAp19, and demonstrate that MAp19 and MASP-2 are encoded by two different mRNA species generated by alternative splicing/polyadenylation from one structural gene.

Molecular basis of human complement C1s deficiency

This is the first report on the molecular basis of human complement C1s deficiency. Two abnormalities in the C1s gene were identified in a Japanese family, including one patient, by using exon-specific PCR, single-strand conformation polymorphism analysis, and nucleotide sequencing. A deletion of 4 bp, TTTG, was identified in exon X when using genomic DNA from the patient, his father, and his paternal grandmother. They were all heterozygous for the mutation. The mutant gene encodes a truncated C1s from the N terminus to the short consensus repeat domain. By further sequencing the PCR products, a nonsense mutation from G to T was identified at codon 608 in exon XII in the patient, his mother, and his sister. They were all heterozygous for the nonsense mutation. The mutant gene encodes a truncated form of C1s that lacks the C-terminal 80 amino acids. These results indicate that the patient was a compound heterozygote with the 4-bp deletion on the paternal allele and the nonsense mutation on the maternal allele. The levels of serum C1s seem to be correlated to the genotypes of the C1s gene in which no C1s was detected in the patient, and one-half of the normal level in the family members who are heterozygous for either mutation. The present study demonstrates that the disease is inherited in an autosomal recessive mode.

Genes regulating MHC class I processing of antigen

The principal pathway of antigen processing that is associated with MHC class I involves three main steps: cytosolic peptide generation, peptide transport into the endoplasmic reticulum and peptide assembly with class I molecules. Recent advances suggest that additional cytosolic proteases complement the proteasome as a source of antigenic peptides. Peptide assembly involves several novel cofactors - including the proteins tapasin and ERp57, which may be important for stabilisation of empty class I molecules as well as quality control after peptide binding. Finally, genetic evidence suggests an important influence of an unidentified gene, in the MHC complex, on MHC class I processing.

Linkage of the NKG2 and CD94 receptor genes to D12S77 in the human natural killer gene complex

The human natural killer (NK) gene complex is located on the short arm of chromosome 12 and contains a number of genes encoding C-type lectin receptors important for natural killer cell function. Among these are CD94 and the five NKG2 genes. The CD94 protein associates with different NKG2 isoforms to heterodimeric receptors which function to inhibit or trigger cytotoxicity of NK cells depending on the NKG2 isoform. We selected two yeast artificial chromosome clones comprising approximately 1.5 Mb of the NK gene complex and established a contig of underlying P1-derived artificial chromosome clones containing all NKG2 and the CD94 genes. A detailed analysis shows that all six genes are found within a region of 100 to 200 kilobases proximal of the marker D12S77. The gene order established is D12S77 - CD94 - NKG2D - NKG2F - NKG2E - NKG2C - NKG2A. The NKG2 genes are of identical transcriptional orientation, whereas the CD94 gene is placed in opposite orientation. The tight genomic linkage of these genes and the identical orientation of the NKG2 genes suggest coordinate regulation of expression during the differentiation of natural killer cells.

Construction of an approximately 700-kb transcript map around the familial Mediterranean fever locus on human chromosome 16p13.3

We used a combination of cDNA selection, exon amplification, and computational prediction from genomic sequence to isolate transcribed sequences from genomic DNA surrounding the familial Mediterranean fever (FMF) locus. Eighty-seven kb of genomic DNA around D16S3370, a marker showing a high degree of linkage disequilibrium with FMF, was sequenced to completion, and the sequence annotated. A transcript map reflecting the minimal number of genes encoded within the approximately 700 kb of genomic DNA surrounding the FMF locus was assembled. This map consists of 27 genes with discreet messages detectable on Northerns, in addition to three olfactory-receptor genes, a cluster of 18 tRNA genes, and two putative transcriptional units that have typical intron-exon splice junctions yet do not detect messages on Northerns. Four of the transcripts are identical to genes described previously, seven have been independently identified by the French FMF Consortium, and the others are novel. Six related zinc-finger genes, a cluster of tRNAs, and three olfactory receptors account for the majority of transcribed sequences isolated from a 315-kb FMF central region (between D16S468/D16S3070 and cosmid 377A12). Interspersed among them are several genes that may be important in inflammation. This transcript map not only has permitted the identification of the FMF gene (MEFV), but also has provided us an opportunity to probe the structural and functional features of this region of chromosome 16.

Chromosome location of genes encoding human blood groups

The chromosomal locations of genes controlling the expression of some 200 antigens constituting the 23 established human blood group systems have been reviewed. Twenty-one of the these genes are located on 12 autosomes, and two are located on the X chromosome. Refined chromosomal positions, to a single cytogenetically distinguishable band, have been established for 13 of the 23 genes. For the remainder, continued investigation will achieve the same result. The genes (RD, MER2, and OK) controlling the expression of one low-incidence and two high-incidence erythrocyte antigens have also been presented. Of these, OK is the most likely candidate for blood group system status, because its chromosomal location distinguishes it from all established system genes except LE and LW, and, the product of the OK gene is different from those of LE and LW (Table 3). This issue will be considered at the next meeting (scheduled for July 1998) of the ISBT Working Party. Alternatively, RD and MER2 are not good candidates for blood group system status because RD and MER2 reside in chromosomal regions containing genes for other blood group systems. In addition, the products of RD and SC have similar biochemical characteristics, and the product of MER2 has not yet been defined (Table 3). The challenge remaining for blood group scientists is characterization of genes that control expression of the approximately 50 other known erythrocyte antigens. Most of these are members of the ISBT's 700 (low-incidence) or 901 (high-incidence) series. Because the current genetic information for each of these antigens (attained by serologic investigation) varies considerably, future studies will have to rely on "tools" from related disciplines to provide the additional information. Use of resources such as molecular biological protocols and GBD should facilitate the effort.

Chromatin remodeling of the interleukin-2 gene: distinct alterations in the proximal versus distal enhancer regions

Known transcription factor-DNA interactions in the minimal enhancer of the murine interleukin-2 gene (IL-2) do not easily explain the T cell specificity of IL-2 regulation. To seek additional determinants of cell type specificity, in vivo methodologies were employed to examine chromatin structure 5' and 3' of the 300 bp IL-2 proximal promoter/enhancer region. Restriction enzyme accessibility revealed that until stimulation the IL-2 proximal promoter/enhancer exists in a closed conformation in resting T and non-T cells alike. Within this promoter region, DMS and DNase I genomic footprinting also showed no tissue-specific differences prior to stimulation. However, DNase I footprinting of the distal -600 to -300 bp region revealed multiple tissue-specific and stimulation-independent DNase I hypersensitive sites. Gel shift assays detected T cell-specific complexes binding within this region, which include TCF/LEF or HMG family and probable Oct family components. Upon stimulation, new DNase I hypersensitive sites appeared in both the proximal and distal enhancer regions, implying that there may be a functional interaction between these two domains. These studies indicate that a region outside the established IL-2 minimal enhancer may serve as a stable nucleation site for tissue-specific factors and as a potential initiation site for activation-dependent chromatin remodeling.

Regulation of IL-18 (IFN-gamma-inducing factor) gene expression

IL-18 (also known as IFN-gamma-inducing factor), although structurally unrelated to IL-12, shares with it the role of activating NK cells and polarizing T cells toward Th1 cell function. To understand how the IL-18 gene (and consequently Th1 function) is regulated, we have determined the gene structure and investigated the mechanisms of transcriptional control and cell type expression. The mouse IL-18 gene comprises seven exons distributed over 26 kb. Exons 1 and 2 of this gene are 5'-noncoding exons. Promoter activity was detected upstream of these noncoding exons in two distinct regions. Both promoters are TATA-less and not G+C rich. The promoter activity located upstream of exon 2 was shown to act constitutively, while the activity located upstream of exon 1 was up-regulated in activated macrophage and T cell lines. IL-18 gene expression may be regulated in a wide range of cell types by the activities of these two distinct promoters. IL-18 is known to be synthesized as a precursor, pro-IL-18, and its maturation is controlled by IL-1beta-converting enzyme (ICE). We observed concordant expression of IL-18 and ICE mRNAs in a wide range of cell types, unlike the more restricted expression of IL-12 p40 mRNA. The widespread IL-18 mRNA distribution and the special relationship with ICE lead us to the hypothesis that IL-18 expression may be coupled with apoptotic processes involving activation of ICE or ICE-like proteinase.

A gain of novel tissue specificity in the human Ly-6 gene E48

The Ly-6 Ag family consists of glycosyl-phosphatidylinositol-anchored surface proteins with a molecular mass of about 15 kDa. Seven members of the murine family have been characterized, and from five of these the genes have been cloned. Three members of the human family have been characterized: CD59, Ag E48, and the RIG-E or TSA-1/Sca-2 Ag. Most of the genes are expressed on lymphocytes, but some are expressed on other tissues as well. The mapped genes of the murine Ly-6 Ags, as well as of CD59, were shown to have a highly conserved structure, each consisting of four exons. The human E48 Ag was originally identified as a target Ag for radioimmunotherapy of patients with squamous cell carcinoma. The Ag is expressed on keratinocytes, but evidently not on lymphocytes. Molecular cloning of the cDNA encoding the Ag revealed that this Ag is most likely the human homologue of the murine Ly-6 Ag, ThB. In this paper, we describe that, in contrast to all other Ly-6 genes, the gene encoding the human E48 Ag consists of only three exons. Sequences at the 5' end of the transcription start site were shown to drive keratinocyte-associated expression. These data suggest that the functional elimination of an ancestral Ly-6 exon 1 switched the expression from lymphocytes toward keratinocytes.

Immunochemical characterization of a novel mitochondrially located protein encoded by a nuclear gene within the DFNB8/10 critical region on 21q22.3

A novel protein encoded by the C210RF2 gene in chromosomal locus 21q22.3 was characterized by immunochemistry. This chromosomal region is known to contain genes for human diseases such as non-syndromic autosomal recessive deafness (DFNB8/10) and autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). Polyclonal murine antisera were produced against the multivalent peptides deduced from the amino acid sequence of the polypeptide. Immunological reactivity of the obtained antisera was tested with primary cells or established cell lines. On western blotting, the polyclonal sera recognized a single protein product of 25 Kd expressed in cell lines of epithelial and lymphoid origin. Subsequent immunochemistry of several human tissues indicated the ubiquitous expression of the protein. Immunofluorescence studies and co-staining with a mitochondrial-specific dye suggest the subcellular localization of the protein to mitochondria. Mitochondrial localization is also predicted by computer analysis of the polypeptide sequence. As deafness is known to be caused in some instances by defects in mitochondrial function, C210RF2 is a plausible candidate gene for DFNB8/10.

Distinct methylation states of the CD8 beta gene in peripheral T cells and intraepithelial lymphocytes

The CD8 coreceptor is expressed on both immature and mature T cells as either an alphabeta heterodimer or an alpha alpha homodimer. Thymocytes and peripheral T cells express CD8 alphabeta, whereas TCR alphabeta+ intraepithelial lymphocytes (IEL) express CD8 alpha alpha or CD8 alphabeta, and the majority of TCR gammadelta+ IEL bear CD8 alpha alpha. The presence of CD8 beta enhances the signaling and adhesion properties of the CD8 alphabeta coreceptor and is necessary for efficient T cell development in the thymus, but is not required for the extrathymic maturation of CD8 alpha alpha+ IEL. To address whether CD8 alpha alpha+ IEL express CD8 beta during their development, we examined the methylation state of cytosines in the CD8 beta gene 5' regulatory region to identify those for which the methylation state inversely correlates with expression of the CD8 beta protein. We identified four such cytosines that were demethylated in CD8 beta-expressing thymocytes and T cells. Interestingly, these cytosines were also demethylated in CD4+ lymph node T cells that had transiently expressed CD8 beta during their development. The methylation state of these cytosines was examined in DNA purified from TCR alphabeta+ CD8 alpha alpha+ and TCR alphabeta+ CD8 alphabeta+ IEL, as well as from TCR gammadelta+ CD8 alpha alpha+ and CD3- CD8 alpha alpha+ IEL. The methylation pattern for TCR alphabeta+ CD8 alpha alpha+ IEL DNA was distinct from that seen for DNA from CD4+ lymph node cells, suggesting that TCR alphabeta+ CD8 alpha alpha+ IEL have not previously expressed CD8 beta. Analysis of DNA from CD3- CD8 alpha alpha+ IEL indicated that the unique methylation pattern of the CD8 beta gene in TCR alphabeta+ CD8 alpha alpha+ IEL DNA was not due to transcription of the CD8 alpha gene or the influence of the gut microenvironment.

Regional localization of ERG, the channel protein responsible for the rapid component of the delayed rectifier, K+ current in the ferret heart

Repolarization of the cardiac action potential varies widely throughout the heart. This could be due to the differential distribution of ion channels responsible for repolarization, especially the K+ channels. We have therefore studied the cardiac localization of ERG, a channel protein known to play an important role in generation of the rapid component of the delayed rectifier K+ current (IKr), an important determinant of the repolarization waveform, Cryosections of the ferret atrium and ventricle were prepared to determine the localization of ERG by fluorescence in situ hybridization (FISH) and immunofluorescence. We found that in the ferret, ERG transcript and protein expression was most abundant in the epicardial cell layers throughout most of the ventricle, except at the base. In the atrium, we found that ERG is most abundant in the medial right atrium, especially in the trabeculae and the crista terminalis of the right atrial appendage. It also is present in areas within the sinoatrial node. In all regions studied, FISH and immunofluorescence showed concordant localization patterns. These data suggest that repolarization mediated by IKr is not uniform throughout the ferret heart and provide a molecular explanation for heterogeneity in action potential repolarization throughout the mammalian heart.

Partitioning of genetic variation between regulatory and coding gene segments: the predominance of software variation in genes encoding introvert proteins

In considering genetic variation in eukaryotes, a fundamental distinction can be made between variation in regulatory (software) and coding (hardware) gene segments. For quantitative traits the bulk of variation, particularly that near the population mean, appears to reside in regulatory segments. The main exceptions to this rule concern proteins which handle extrinsic substances, here termed extrovert proteins. The immune system includes an unusually large proportion of this exceptional category, but even so its chief source of variation may well be polymorphism in regulatory gene segments. The main evidence for this view emerges from genome scanning for quantitative trait loci (QTL), which in the case of the immune system points to a major contribution of pro-inflammatory cytokine genes. Further support comes from sequencing of major histocompatibility complex (Mhc) class II promoters, where a high level of polymorphism has been detected. These Mhc promoters appear to act, in part at least, by gating the back-signal from T cells into antigen-presenting cells. Both these forms of polymorphism are likely to be sustained by the need for flexibility in the immune response. Future work on promoter polymorphism is likely to benefit from the input from genome informatics.

Specific versus cooperative regulatory mechanisms of the cytokine genes that are clustered on the same chromosome

The genes for IL-3, IL-4, IL-5, IL-9, IL-13, and granulocyte-macrophage colony-stimulating factor (GM-CSF) are known to be clustered on human chromosome 5q and on mouse chromosome 11. IL-2 and interferon gamma (IFN-gamma) genes are located on separate chromosomes. It is well known that upon stimulation by antigen presentation, TH1 and TH2 subsets of T helper cells start to transcribe distinct sets of cytokine genes. Thus mechanisms should exist that transmit extracellular signals into the nucleus, thereby coordinately turning on transcriptional machinery in cell type-specific manners. Several different mechanisms exist in which specific as well as coordinated expression of cytokines are regulated at the transcriptional level. These include (1) regulation by proximal cis-elements, to which specific transcription factors bind, (2) regulation by distal cis-elements, such as enhancers or locus controlling elements, especially those located several kilobases away from the target gene, and (3) enhancement of transcription by viral trans-activators in a pathologic state. In this article, we review the recent studies on the above issues, with particular emphasis on our own results that support the presence of different modes of control mechanisms. We also discuss the possible approaches to the thorough understanding of the coordinated and specific regulation of cytokines.

Stable transfection of cloned murine T helper cells

Here we describe a protocol for the stable transfection of murine T helper (Th) cells and long term culture of the resulting transfectants. The electroporation protocol was established for the murine Th2 clone L1/1 by testing different parameters determining the electric field (capacitance, voltage, single or twin pulse) as well as the activation status of the cells. The transfected T cells were genetically altered by stable integration of the neomycin resistance gene, encoded in the vector pM5neo, into the genome. For selection and long term culture of stable transfectants a scheme combining selection with the antibiotic neomycin (G-418, Geneticin) and repeated stimulation with antigen presenting cells (APC) and antigen was established. This protocol should also be applicable to other antigen reactive T cells. The resistance of the T cells to neomycin correlated directly with expression of the transferred neomycin resistance gene as demonstrated by mRNA analysis. Applying periodic reselection with neomycin the transfected Th2 cells were found to be stable for more than 18 months in culture and displayed an unaltered antigen recognition and lymphokine production pattern as compared with the untransfected L1/1 Th2 cells.

Expression and functional properties of mouse B7/BB1 using a fusion protein between mouse CTLA4 and human gamma 1

We report the construction and expression of a fusion protein made from the extracellular portion of the mouse CTLA-4 gene and the constant region of human IgG1. This fusion protein behaves like an antibody to mouse B7/BB1, binding to activated B cells and purified dendritic cells. In addition, we found it to bind to activated T cells. The fusion protein interfered with the ability of antigen-pulsed antigen-presenting cells to induce proliferation of T-cell clones, although the degree of inhibition varied. These findings are discussed in the light of the physiological activation of T cells in secondary lymphoid organs.

Characterization of T-cell receptor gamma delta T cells appearing at the early phase of murine Listeria monocytogenes infection

It has been shown that T-cell receptor (TcR) gamma delta + CD4- CD8- T cells increase in number and have an important role in early protection in murine Listeria monocytogenes infection. In this report, to characterize further the phenotype of the gamma delta T cells in listeriosis, we analysed V region gene usage and in vitro antigen recognition of the TcR gamma delta T cells in the peritoneal cavity of mice at the early phase after i.p. infection with a sublethal dose of L. monocytogenes. The gamma delta T cells predominantly expressed V delta 6 which has been reported to be expressed by TcR gamma delta-bearing foetal thymocyte hybridomas specific to mycobacterial and self heat-shock protein (hsp) 60. These early appearing CD3+ CD4- CD8- T cells in Listeria-infected mice, which were reported to be TcR gamma delta T cells, increased in proportion and in size by in vitro stimulation with recombinant hsp 60 from Mycobacterium bovis and purified protein derivative from M. tuberculosis but not by stimulation with heat-killed L. monocytogenes. A 65,000 MW molecule was detected in the lysate of viable L. monocytogenes but not in the lysate of heat-killed L. monocytogenes by a monoclonal antibody (mAb) raised against mycobacterial hsp 60. These results suggest that the V delta 6-bearing peripheral gamma delta T cells are activated by recognizing listerial hsp 60 expressed by viable L. monocytogenes. The hsp 60-reactive V delta 6-bearing T cells may have an important role in protection against L. monocytogenes and other parasites that express hsp 60 at high level.

Haematopoietic cell lines capable of colonizing the thymus following in vivo transfer expressed T-cell receptor gamma-gene immature mRNA

To clarify the mechanism by which progenitor T (pro-T) cells recognize and enter the thymus, an attempt was made to produce haematopoietic cell lines by the fusion of BALB/c nude mouse bone marrow or foetal liver cells (gestation 14 and 15 days) with AKR thymoma BW5147, thereby immortalizing cells with potency to colonize the thymus, a characteristic of pro-T cells rarely found in adult bone marrow or foetal liver. The hybridomas thus produced were classified according to the phenotype of surface markers, T-cell receptor (TcR) gene configuration and expression. All hybridomas were negative in the surface expression of T-cell markers such as TcR alpha beta, TcR gamma delta, CD3, CD4 and CD8. They had TcR beta-, gamma- and delta-genes, each with a different status with respect to configuration and transcription. Some possessed partially rearranged TcR genes and others expressed immature TcR mRNA. The cell lines were examined for their capacity to colonize the thymus following intravenous injection into recipient mice. It was found that the cells with capacity of colonizing the thymus expressed immature TcR delta mRNA, while the cell lines lacking TcR delta-genes did not home to the thymus. These findings imply that the potency for migrating to thymus is closely associated with the particular stage of prethymic cell differentiation which could be estimated by the analysis of TcR genes, and that some cell lines with the expression of TcR delta-gene mRNA and the ability to colonize the thymus are derived from pro-T cells.