Analysis of the B cell receptor repertoire in six immune-mediated diseases.

B cells are important in the pathogenesis of many, and perhaps all, immune-mediated diseases. Each B cell expresses a single B cell receptor (BCR)1, and the diverse range of BCRs expressed by the total B cell population of an individual is termed the 'BCR repertoire'. Our understanding of the BCR repertoire in the context of immune-mediated diseases is incomplete, and defining this could provide new insights into pathogenesis and therapy. Here, we compared the BCR repertoire in systemic lupus erythematosus, anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis, Crohn's disease, Behçet's disease, eosinophilic granulomatosis with polyangiitis, and immunoglobulin A (IgA) vasculitis by analysing BCR clonality, use of immunoglobulin heavy-chain variable region (IGHV) genes and-in particular-isotype use. An increase in clonality in systemic lupus erythematosus and Crohn's disease that was dominated by the IgA isotype, together with skewed use of the IGHV genes in these and other diseases, suggested a microbial contribution to pathogenesis. Different immunosuppressive treatments had specific and distinct effects on the repertoire; B cells that persisted after treatment with rituximab were predominately isotype-switched and clonally expanded, whereas the inverse was true for B cells that persisted after treatment with mycophenolate mofetil. Our comparative analysis of the BCR repertoire in immune-mediated disease reveals a complex B cell architecture, providing a platform for understanding pathological mechanisms and designing treatment strategies.

Expression profiling of Sudanese visceral leishmaniasis patients pre- and post-treatment with sodium stibogluconate.

Visceral leishmaniasis (VL) in Sudan caused by Leishmania donovani is fatal in susceptible individuals if untreated. Treatment with sodium stibogluconate (SSG) leads to post-kala-azar dermal leishmaniasis (PKDL) in 58% of patients. Here, Affymetrix microarrays were used to identify genes differentially expressed in lymph nodes (N=9 paired samples) pre- and post-treatment with SSG. Using the Bioconductor package limma, 438 genes from 28 869 post-quality-control probe sets were differentially expressed (Pnominal ≤.02) post- vs pretreatment. Canonical pathway analysis using Ingenuity Pathway Analysis™ identified "role of nuclear factor of activated T-cell in regulation of immune response" (Pnominal =1.35×10-5 ; PBH-adjusted =4.79×10-3 ), "B-cell development" (Pnominal =2.04×10-4 ; PBH-adjusted =.024), "Fcγ receptor-mediated phagocytosis in macrophages and monocytes" (Pnominal =2.04×10-4 ; PBH-adjusted =.024) and "OX40 signalling" (Pnominal =2.82×10-4 ; PBH-adjusted =.025) as pathways differentially regulated post- vs pretreatment. Major network hub genes included TP53, FN1, MYC, BCL2, JUN, SYK, RUNX2, MMP1 and ACTA2. Top endogenous upstream regulators included IL-7 (P=2.28×10-6 ), TNF (P=4.26×10-6 ), Amyloid Precursor Protein (P=4.23×10-5 ) and SPI1/PI.1 (P=1.17×10-7 ). Top predicted chemical drug regulators included the flavonoid genistein (P=4.56×10-7 ) and the quinoline alkaloid camptothecin (P=5.14×10-5 ). These results contribute to our understanding of immunopathology associated with VL and response to SSG treatment. Further replication could identify novel therapeutic strategies that improve on SSG treatment and reduce the likelihood of progression to PKDL.

Effects of galactose feeding on aldose reductase gene expression.

Aldose reductase (AR) is implicated in the pathogenesis of the diabetic complications and osmotic cataract. AR has been identified as an osmoregulatory protein, at least in the renal medulla. An outstanding question relates to the response of AR gene expression to diet-induced galactosemia in extrarenal tissues. This paper shows that AR gene expression in different tissues is regulated by a complex multifactorial mechanism. Galactose feeding in the rat is associated with a complex and, on occasions, multiphasic pattern of changes in AR mRNA levels in kidney, testis, skeletal muscle, and brain. These changes are not in synchrony with the temporal sequence of changes in tissue galactitol, galactose, and myoinositol concentrations. Moreover, galactose feeding results in changes in tissue AR activities that are not related, temporally or quantitatively, to the alterations in tissue AR mRNA or galactitol levels. It is concluded that AR gene expression and tissue AR activities are regulated by mechanisms that are not purely dependent on nonspecific alterations in intracellular metabolite concentrations. This conclusion is supported by the finding that chronic xylose feeding, despite being associated with intracellular xylitol accumulation, does not result in alterations in AR mRNA levels, at least in the kidney.

Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis.

Conventional approaches to target labelling for expression microarray analysis typically require relatively large amounts of total RNA, a serious limitation when the sample available is small. Here we explore the cycle-dependent amplification characteristics of Template-Switching PCR and validate its use for microarray target labelling. TS-PCR identifies up to 80% of the differentially expressed genes identified by direct labelling using 30-fold less input RNA for the amplification, with the equivalent of 1000-fold less starting material being used for each hybridisation. Moreover, the sensitivity of microarray experiments is increased considerably, allowing the identification of differentially expressed transcripts below the level of detection using targets prepared by direct labelling. We have also validated the fidelity of amplification and show that the amplified material faithfully represents the starting mRNA population. This method outperforms conventional labelling strategies, not only in terms of sensitivity and the identification of differentially expressed genes, but it is also faster and less labour intensive than other amplification protocols.

Analysis of the mouse CD30 gene: a candidate for the NOD mouse type 1 diabetes locus Idd9.2.

Members of the tumor necrosis factor receptor superfamily play an important role in the initiation, expansion, and termination of an immune response. It has recently been demonstrated that one member of this family, CD30, plays a central role in maintaining peripheral tolerance by controlling the expansion of autoreactive CD8+ T-cells. In the present study, Cd30 was mapped to a 5.6-cM interval on chromosome 4 containing the type 1 diabetes susceptibility locus Idd9.2. We determined the intron/exon structure of Cd30 and sequenced the exons, as well as 1.8 kb of the 5' putative promoter region, from 6 different mouse strains. Remarkably, 63 sequence variants, both coding and noncoding, were found. A total of 27 sequence variants, 4 of which were nonsynonymous, were found between the diabetes susceptible NOD strain and the resistant B10 strain. Of these sequence variants, 19 are within the promoter region. However, no difference between NOD and the congenic strain NOD.B10 Idd9R1, which has the B10 allele of Cd30, was observed in CD30 expression at either the mRNA or protein level. Given its role in protecting against autoimmunity, one or more of the coding variants within CD30 is a good candidate for the Idd9.2 etiological variant.

NOD Idd5 locus controls insulitis and diabetes and overlaps the orthologous CTLA4/IDDM12 and NRAMP1 loci in humans.

A genome scan for B10-derived loci that reduce the frequency of diabetes and insulitis in NOD mice demonstrated a large region (34 cM) of linkage on the proximal end of chromosome 1. This locus was designated Idd5 and encompassed candidate genes including Il1r1, Il1r2, Stat1, Stat4, Nramp1, and Bcl2. In the current study, we have confirmed the existence of Idd5 by developing a series of congenic mouse strains that are resistant to diabetes and determined that Idd5 is actually two genes located within a 9.4-cM interval. Idd5.1 is in the proximal 1.5-cM portion of the interval and contains the candidates Casp8, Cflar (FLIP), Cd28, and Cd152 (CTLA4). Idd5.1 overlaps the orthologous CTLA4/IDDM12 locus in humans. Idd5.2 is in the distal 5.1-cM portion of the 9.4-cM interval and contains the candidates Nramp1, which has a functional polymorphism between NOD and B10, and Cmkar2 (CXCR2, interleukin [IL]-8 receptor alpha). Candidate genes eliminated by this analysis include Il1r1, Ilr2, Zap70, Orch5, Stat1, Stat4, Bcl2, Cmkar4 (CXCR4), and Il10. On its own, the Idd5 locus provides a significant amount of protection from diabetes (50% reduction from parental frequency) and when combined with another resistance locus (Idd3 on chromosome 3), provides nearly complete protection from diabetes and insulitis.

Mapping by genetic interaction: high-resolution congenic mapping of the type 1 diabetes loci Idd10 and Idd18 in the NOD mouse.

As many of the linked chromosome regions that predispose to type 1 diabetes in the NOD mouse have been dissected, it has become apparent that the initially observed effect is in fact attributable to several loci. One such cluster of loci on distal chromosome 3, originally described as Idd10, is now known to comprise three separate loci, Idd10, Idd17, and Idd18. Although these loci have a significant combined effect on diabetes development, their individual effects are barely detectable when diabetes is used as a read-out, which makes fine-mapping them by use of a conventional congenic approach impractical. In this study, we demonstrate that it is possible to map loci, with modest effects, to regions small enough for systematic gene identification by capitalizing on the fact that the combined loci provide more profound, measurable protection. We have mapped the Idd10 and Idd18 loci to 1.3- and 2.0-cM intervals, respectively, by holding the Idd3 allele constant. In addition, we have excluded Csf1 and Nras as candidates for both loci.

Mapping of the IDDM locus Idd3 to a 0.35-cM interval containing the interleukin-2 gene.

Currently, 16 loci that contribute to the development of IDDM in the NOD mouse have been mapped by linkage analysis. To fine map these loci, we used congenic mapping. Using this approach, we localized the Idd3 locus to a 0.35-cM interval on chromosome 3 containing the Il2 gene. Segregation analysis of the known variations within this interval indicated that only one variant, a serine-to-proline substitution at position 6 of the mature interleukin-2 (IL-2) protein, consistently segregates with IDDM in crosses between NOD and a series of nondiabetic mouse strains. These data, taken together with the immunomodulatory role of IL-2, provide circumstantial evidence in support of the hypothesis that Idd3 is an allelic variation of the Il2 gene, or a variant in strong linkage disequilibrium.

Statistical modeling of interlocus interactions in a complex disease: rejection of the multiplicative model of epistasis in type 1 diabetes.

In general, common diseases do not follow a Mendelian inheritance pattern. To identify disease mechanisms and etiology, their genetic dissection may be assisted by evaluation of linkage in mouse models of human disease. Statistical modeling of multiple-locus linkage data from the nonobese diabetic (NOD) mouse model of type 1 diabetes has previously provided evidence for epistasis between alleles of several Idd (insulin-dependent diabetes) loci. The construction of NOD congenic strains containing selected segments of the diabetes-resistant strain genome allows analysis of the joint effects of alleles of different loci in isolation, without the complication of other segregating Idd loci. In this article, we analyze data from congenic strains carrying two chromosome intervals (a double congenic strain) for two pairs of loci: Idd3 and Idd10 and Idd3 and Idd5. The joint action of both pairs is consistent with models of additivity on either the log odds of the penetrance, or the liability scale, rather than with the previously proposed multiplicative model of epistasis. For Idd3 and Idd5 we would also not reject a model of additivity on the penetrance scale, which might indicate a disease model mediated by more than one pathway leading to beta-cell destruction and development of diabetes. However, there has been confusion between different definitions of interaction or epistasis as used in the biological, statistical, epidemiological, and quantitative and human genetics fields. The degree to which statistical analyses can elucidate underlying biologic mechanisms may be limited and may require prior knowledge of the underlying etiology.

Activation of erythrocyte aldose reductase in man in response to glycaemic challenge.

Flux via the polyol pathway, which comprises the enzymes aldose reductase (AR) and sorbitol dehydrogenase (SDH), has been implicated in the debilitating complications of diabetes. Previous studies in this laboratory have indicated that erythrocyte AR activities are increased (by 72%) in insulin-dependent diabetic patients. To investigate the mechanism underlying this activation, the response of AR activity to oral glucose challenge was investigated in eight overnight-fasted human volunteers. Glucose consumption led to a transient activation (by 76%: P less than 0.01) of erythrocyte AR, which paralleled the rise and subsequent fall in blood glucose concentrations. It is concluded that erythrocyte AR activity is acutely modulated in response to hyperglycaemia by an as yet unknown mechanism.

Mouse chromosome 3.

> http://link.springer-ny. com/link/service/journals/00335/bibs/10n10p942.html

Identification of the glycoprotein H gene of murine cytomegalovirus.

Partial sequencing of the HindIII C fragment of murine cytomegalovirus (MCMV) revealed an open reading frame of 2172 nucleotides in length encoding a 724 amino acid protein with a predicted Mr of 80.4K. Analysis of the predicted amino acid sequence revealed homology with glycoprotein H (gH) from a number of other herpesviruses. MCMV gH showed strongest amino acid identity with human (H) CMV and human herpesvirus 6 gH, and less identity with the gH protein sequences of Epstein-Barr virus, varicella-zoster virus and herpes simplex virus type 1. The greatest identity between MCMV and HCMV gH occurs in the C-terminal region. The MCMV gH is characterized by having a 14 amino acid signal sequence, a 23 amino acid transmembrane region, a seven amino acid positively charged cytoplasmic anchor sequence and eight putative N-linked glycosylation sites. Comparison of MCMV gH with that of HCMV indicates that there are 12 conserved cysteine residues and three conserved potential N-linked glycosylation sites.

Effect of natural sequence variation at the H-2Ld-restricted CD8+ T cell epitope of the murine cytomegalovirus ie1-encoded pp89 on T cell recognition.

The amino acid sequence YPHFMPTNL of pp89, the ie1-encoded product of murine cytomegalovirus (MCMV; Smith strain), constitutes an immunodominant T cell epitope recognized in association with H-2Ld. Nucleotide sequencing of MCMV isolates derived from wild mice identified variation between amino acids 147-192 of pp89 in 19 of 27 isolates, including the region encompassing the CTL epitope (amino acid residues 168-176). Four groups of isolates with naturally occurring variant sequences for the CTL epitope were defined: (1) YPHFMPPNL; (2) YPHFMPPSL; (3) YPHFIPPSL; and (4) YLDFMPPNL. The remaining isolates, and the laboratory strains K181 and Vancouver, showed complete identity with the Smith strain. Polyclonal pp89 (Smith strain)-specific CTL only weakly recognized target cells infected with MCMV from most variant groups. No lysis of cells infected with isolate N1 from group 4 was detected. Analyses of cross-reactive recognition of YPHFMPTNL peptide-coated targets by CTL primed with variant MCMV isolates showed that the group 2 and 3 isolates, G4 and K6, respectively, but not the group 4 isolate N1, elicited CTL that exhibited a cross-reactive response. Furthermore, while the group 2 and 3 isolates G4 and K6 were able to prime CTL responses that displayed reactivity to homologous pp89 variant nonapeptides, the group 4 isolate N1 failed to do so. Finally, while immunization of mice with the nonapeptide YPHFMPTNL conferred significant protection against the laboratory strain K181 [correction of Kl81], no evidence of protection was observed for the group 2 and 4 variants G4 and N1, respectively. These observations raise the possibility that clinical isolates of HCMV may also differ in sequence from potential vaccine strains at immunodominant epitopes for CD8+ T cells thus reducing the efficacy of vaccination.

Expression of the glycoprotein H of murine cytomegalovirus and identification of an N-terminal antibody-binding region.

A series of overlapping fragments spanning the entire coding sequence of the gH gene of murine cytomegalovirus (MCMV) were expressed in Escherichia coli as fusion proteins with glutathione S-transferase (GST) using the pGEX expression system. A region of antibody-binding was mapped to the NH2-terminus of glycoprotein H (gH) between amino acid residues 26 and 90 on the basis of the reactivity of GST-gH fusion proteins with polyclonal antibodies to MCMV in Western blot analysis. Antibodies to gH were generated in mice immunized with the GST-gH fusion protein SK and shown to react with an 87-kDa polypeptide present in virion particles which was conserved in MCMV isolates obtained from diverse locations. They also recognized the gH protein in MCMV-infected cells, as well as gH expressed in Chinese Hamster Ovary cells. The antibodies to gH had a significant ELISA titer but no neutralizing activity in vitro. The antibody response to the GST-gH fusion protein did not modify the level of MCMV replication in the spleens of mice.

Mapping and transcriptional analysis of the murine cytomegalovirus homologue of the human cytomegalovirus UL103 open reading frame.

Murine cytomegalovirus (MCMV) has been widely used as a model for human cytomegalovirus (HCMV) infection since the two viruses share many biological and pathogenic properties. To further evaluate the similarities in the genomes of these viruses we have sought to identify MCMV genes that encode immunoreactive proteins by screening a lambda gt11 cDNA library with anti-MCMV monoclonal antibodies (MAb). Clone 430, identified on the basis of its reactivity with the MAb 6/20/1, was completely sequenced and shown to encode the MCMV homologue of the HCMV UL103 open reading frame (ORF). This ORF is encoded by a 1.1-kb transcript that is expressed at late times following infection. Sequencing of the cDNA also revealed the presence of two incomplete ORFs encoding the homologues of the HCMV UL102 and 104 ORFs. These ORFs are encoded by a 2.4-kb leaky late transcript and a 3.0-kb late transcript, respectively. Together these ORFs constitute part of a block of genes conserved in all herpesviruses, and in the MCMV and HCMV genomes this block of genes shows striking positional homology. The high degree of homology between HCMV and MCMV ORFs, at both the nucleotide and amino acid levels, plus the growing evidence of conservation in gene order between the two genomes suggests that the two viruses are very similar at the molecular level.

Genetic mapping of Cmv1 in the region of mouse chromosome 6 encoding the NK gene complex-associated loci Ly49 and musNKR-P1.

The Cmv1 resistance gene controls splenic replication of murine cytomegalovirus (MCMV) and confers natural killer (NK) cell-mediated resistance to otherwise lethal infection. The Cmv1 phenotypes of 13 inbred mouse strains have been assessed, and it was found that the Cmv1r resistance phenotype was restricted to the C57BL/6J and Ma/MyJ strains. We have further analyzed the linkage of Cmv1 to the NK gene complex (NKC) mapping to distal mouse chromosome 6 in 99 (BALB/c x C57BL/6J)F1 x BALB/c backcross mice using cloned gene probes and microsatellite markers from this region. No recombinants were observed between Cmv1 and the NKC-associated Ly49 and musNKR-P1 multigene families, nor the Kap locus, nor with 7 microsatellite markers, indicating that Cmv1 is closely linked (< 1 cM) to all of these markers. Analysis of the genotype of the MCMV-susceptible BXD8 RI strain around the NKC region revealed that it had C57BL/6J alleles at microsatellite markers immediately proximal and distal to Cmv1. This suggests that the Cmv1s phenotype of this strain is due to a germ-line mutation. Thus, the close linkage of Cmv1 to the Ly49 and musNKR-P1 multigene families suggests that it may represent an NK cell recognition structure encoded in the NKC region.

DNA sequence and transcriptional analysis of the glycoprotein M gene of murine cytomegalovirus.

We have characterized the gene encoding the murine cytomegalovirus (MCMV) homologue of the human cytomegalovirus (HCMV) UL100 open reading frame (ORF) that encodes the HCMV glycoprotein M (gM) molecule. It was identified based on its collinearity with MCMV homologues of the HCMV UL99, UL102, UL103 and UL104 ORFs which lie in the HindIII G fragment of the K181 strain of MCMV. Sequencing of a 2.3 kb EcoRI-BamHI subfragment of the EcoRI G fragment adjacent to the EcoRI A fragment revealed the presence of the complete MCMV gM ORF and two incomplete ORFs, which corresponded to homologues of HCMV UL99 and UL102. The MCMV gM ORF consists of 1059 nucleotides and is expressed as a 1.2 kb transcript at late times post-infection. To precisely characterize the gM transcript, the 5' and 3' ends were mapped. It was found that the transcript initiates at nucleotides 740 or 745, and that the site of polyadenylation at nucleotide 1961 occurs downstream of the second potential polyadenylation signal located at nucleotide 1934. Based on these findings the MCMV gM is predicted to consist of 353 residues and when compared with HCMV gM has a 47% level of identity. Of great interest is the finding that the MCMV gM amino acid sequence is completely conserved among six isolates of MCMV that had been shown to exhibit considerable variation both in the MCMV glycoprotein B and the immediate-early 1 gene-encoded pp89 molecule. Thus, this glycoprotein appears to be antigenically conserved.