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Objective To study the effect of the innate cytokine, MIF, on the susceptibility and the severity of SLE in a multinational population of Caucasian and African-American patients. Methods We studied the association between two functional polymorphisms in the MIF gene: a −794 CATT5-8 microsatellite repeat (rs5844572) and a −173 G/C SNP (rs755622), with SLE in 3195 patients and controls. We also measured MIF plasma levels in relation to genotypes, clinical phenotypes, and TLR 7-stimulated MIF production in vitro. Results Both Caucasians and African-Americans with the high expression, −794 CATT7/173*C haplotype had lower SLE incidence (OR 0.63 [0.53, 0.89], p=0.001 in Caucasians, and OR 0.46 [0.23, 0.95], p=0.012 in African-Americans). By contrast, among patients with established SLE, those with nephritis, serositis, and CNS involvement had reduced frequencies of low expression MIF genotypes (−794 CATT5) when compared to patients without end-organ involvement (p=0.005 for serositis, p=0.023 for nephritis, and p=0.04 for CNS involvement). Plasma MIF levels and TLR7 stimulated MIF production in vitro reflected the underlying MIF genotype of the studied groups. Conclusion These data suggest that MIF, which has both pro-inflammatory properties and macrophage and B cell survival functions, exerts a dual influence on the immunopathogenesis of SLE. High expression MIF genotypes are associated with a reduced susceptibility to SLE and may contribute to an enhanced clearance of infectious pathogens. Once SLE develops however, low expression MIF genotypes may protect from ensuing, inflammatory end-organ damage.

Inter-individual differences in gene expression are likely to account for an important fraction of phenotypic differences, including susceptibility to common disorders. Recent studies have shown extensive variation in gene expression levels in humans and other organisms, and that a fraction of this variation is under genetic control. We investigated the patterns of gene expression variation in a 25 Mb region of human chromosome 21, which has been associated with many Down syndrome (DS) phenotypes. Taqman real-time PCR was used to measure expression variation of 41 genes in lymphoblastoid cells of 40 unrelated individuals. For 25 genes found to be differentially expressed, additional analysis was performed in 10 CEPH families to determine heritabilities and map loci harboring regulatory variation. Seventy-six percent of the differentially expressed genes had significant heritabilities, and genomewide linkage analysis led to the identification of significant eQTLs for nine genes. Most eQTLs were in trans, with the best result (P=7.46 x 10(-8)) obtained for TMEM1 on chromosome 12q24.33. A cis-eQTL identified for CCT8 was validated by performing an association study in 60 individuals from the HapMap project. SNP rs965951 located within CCT8 was found to be significantly associated with its expression levels (P=2.5 x 10(-5)) confirming cis-regulatory variation. The results of our study provide a representative view of expression variation of chromosome 21 genes, identify loci involved in their regulation and suggest that genes, for which expression differences are significantly larger than 1.5-fold in control samples, are unlikely to be involved in DS-phenotypes present in all affected individuals.

The T-cell receptor (TCR) plays a central role in the immune system, and > 90% of human T cells present a receptor that consists of the alpha TCR subunit (TCRA) and the beta subunit (TCRB). Here we report an analysis of 63 variable genes (BV), spanning 553 kb of TCRB that yielded 279 single-nucleotide polymorphisms (SNPs). Samples were drawn from 10 individuals and represent four populations-African American, Chinese, Mexican, and Northern European. We found nine variants that produce nonfunctional BV segments, removing those genes from the TCRB genomic repertoire. There was significant heterogeneity among population samples in SNP frequency (including the BV-inactivating sites), indicating the need for multiple-population samples for adequate variant discovery. In addition, we observed considerable linkage disequilibrium (LD) (r(2) > 0.1) over distances of approximately 30 kb in TCRB, and, in general, the distribution of r(2) as a function of physical distance was in close agreement with neutral coalescent simulations. LD in TCRB showed considerable spatial variation across the locus, being concentrated in "blocks" of LD; however, coalescent simulations of the locus illustrated that the heterogeneity of LD we observed in TCRB did not differ markedly from that expected from neutral processes. Finally, examination of the extended genotypes for each subject demonstrated homozygous stretches of >100 kb in the locus of several individuals. These results provide the basis for optimization of locuswide SNP typing in TCRB for studies of genotype-phenotype association.

Axis formation in Drosophila depends on correct patterning of the follicular epithelium and on signaling between the germ line and soma during oogenesis. We describe a method for identifying genes expressed in the follicle cells with potential roles in axis formation. Follicle cells are purified from whole ovaries by enzymatic digestion, filtration, and f luorescence-activated cell sorting (FACS). Two strategies are used to obtain complementary cell groups. In the first strategy, spatially restricted subpopulations are marked for FACS selection using a green f luorescent protein (GFP) reporter. In the second, cells are purified from animals mutant for the epidermal growth factor receptor ligand gurken (grk) and from their wild-type siblings. cDNA from these samples of spatially restricted or genetically mutant follicle cells is used in differential expression screens employing PCR-based differential display or hybridization to a cDNA microarray. Positives are confirmed by in situ hybridization to whole mounts. These methods are found to be capable of identifying both spatially restricted and grk-dependent transcripts. Results from our pilot screens include (i) the identification of a homologue of the immunophilin FKBP-12 with dorsal anterior expression in egg chambers, (ii) the discovery that the ecdysone-inducible nuclear hormone receptor gene E78 is regulated by grk during oogenesis and is required for proper dorsal appendage formation, and (iii) the identification of a Drosophila homologue of the human SET-binding factor gene SBF1 with elevated transcription in grk mutant egg chambers.Recent years have seen an explosion in tools for analyzing differential gene expression. The development of a PCR-based differential display method by Liang et al. (1, 2) has quickly been followed by array-based methods for monitoring the expression of thousands of defined genes simultaneously (3, 4). Developmental biology, a field whose progress depends heavily on understanding regulated gene expression, stands to benefit from these methods. However, there are technical hurdles to be overcome before molecular screening methods can be widely applied to problems in development. Chief among these hurdles is purification of the tissue of interest from the complex mixture of cell types typically present in a developing system. Whereas some tissues are amenable to microdissection, others will require more sophisticated techniques such as fluorescence-activated cell sorting (FACS) of dissociated tissue (5-7). The molecular screens reported herein rely on a FACS-based approach to purify specialized follicle cells from Drosophila ovaries. The system we have chosen is particularly illustrative of the need for tissue purification: the Drosophila ovary is composed of egg chambers in which a cyst of large germ-line cells is surrounded by a thin epithelium of highly differentiated follicle cells. Patterning of subregions of the follicular epithelium involves intermingled cell groups, each comprising only a tiny fraction of the volume...