Flemming Pociot

Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes

Type 1 diabetes (T1D) is a common autoimmune disorder that arises from the action of multiple genetic and environmental risk factors. We report the findings of a genome-wide association study of T1D, combined in a meta-analysis with two previously published studies. The total sample set included 7,514 cases and 9,045 reference samples. Forty-one distinct genomic locations provided evidence for association with T1D in the meta-analysis (P < 10−6). After excluding previously reported associations, we further tested 27 regions in an independent set of 4,267 cases, 4,463 controls and 2,319 affected sib-pair (ASP) families. Of these, 18 regions were replicated (P < 0.01; overall P < 5 × 10−8) and 4 additional regions provided nominal evidence of replication (P < 0.05). The many new candidate genes suggested by these results include IL10, IL19, IL20, GLIS3, CD69 and IL27.

Cytokine gene polymorphism in human disease: on-line databases

The pathologies of many infectious, autoimmune and malignant diseases are influenced by the profiles of cytokine production in pro-inflammatory (TH1) and anti-inflammatory (TH2) T cells. Interindividual differences in cytokine profiles appear to be due, at least in part, to allelic polymorphism within regulatory regions of cytokine gene. Many studies have examined the relationship between cytokine gene polymorphism, cytokine gene expression in vitro, and the susceptibility to and clinical severity of diseases. A review of the findings of these studies is presented. An on-line version featuring appropriate updates is accessible from the World Wide Web site, http://www.pam.bris.ac.uk/services/GAI/cytokine4.htm.

A human phenome-interactome network of protein complexes implicated in genetic disorders

We performed a systematic, large-scale analysis of human protein complexes comprising gene products implicated in many different categories of human disease to create a phenome-interactome network. This was done by integrating quality-controlled interactions of human proteins with a validated, computationally derived phenotype similarity score, permitting identification of previously unknown complexes likely to be associated with disease. Using a phenomic ranking of protein complexes linked to human disease, we developed a Bayesian predictor that in 298 of 669 linkage intervals correctly ranks the known disease-causing protein as the top candidate, and in 870 intervals with no identified disease-causing gene, provides novel candidates implicated in disorders such as retinitis pigmentosa, epithelial ovarian cancer, inflammatory bowel disease, amyotrophic lateral sclerosis, Alzheimer disease, type 2 diabetes and coronary heart disease. Our publicly available draft of protein complexes associated with pathology comprises 506 complexes, which reveal functional relationships between disease-promoting genes that will inform future experimentation.

Susceptibility to human type 1 diabetes at IDDM2 is determined by tandem repeat variation at the insulin gene minisatellite locus

The IDDM2 locus encoding susceptibility to type 1 diabetes was mapped previously to a 4.1–kb region spanning the insulin gene and a minisatellite or variable number of tandem repeats (VNTR) locus on human chromosome 11p15.5. By ‘cross–match’ haplotype analysis and linkage disequilibrium mapping, we have mapped the mutation IDDM2 to within the VNTR itself. Other polymorphisms were systematically excluded as primary disease determinants. Transmission of IDDM2 may be influenced by parent–of–origin phenomena. Although we show that the insulin gene is expressed biallelically in the adult pancreas, we present preliminary evidence that the level of transcription in vivo is correlated with allelic variation within the VNTR. Allelic variation at VNTRs may play an important general role in human disease.

CTLA-4 IN AUTOIMMUNE DISEASES-A GENERAL SUSCEPTIBILITY GENE TO AUTOIMMUNITY?

For most autoimmune disorders, the pattern of inheritance is very complex. The major histocompatibility complex (MHC) gene complex has been implicated as the major genetic component in the predisposition to these diseases but other genes are likely to be involved. Based on function and experimental data, the gene encoding cytotoxic T lymphocyte-associated antigen 4 (CTLA4) has been suggested as a candidate gene for conferring susceptibility to autoimmunity. In this review, we critically evaluate the evidence for pathogenetical involvement of CTLA-4 in the different autoimmune diseases with focus on the possible role of genetic variation of the CTLA4 locus.

Genetics of type 1 diabetes mellitus

At least 20 different chromosomal regions have been linked to type 1 diabetes (T1D) susceptibility in humans, using genome screening, candidate gene testing, and studies of human homologues of mouse susceptibility genes. The largest contribution from a single locus (IDDM1) comes from several genes located in the MHC complex on chromosome 6p21.3, accounting for at least 40% of the familial aggregation of this disease. Approximately 30% of T1D patients are heterozygous for HLA-DQA1*0501–DQB1*0201/DQA1*0301–DQB1*0302 alleles (formerly referred to as HLA-DR3/4 and for simplification usually shortened to HLA-DQ2/DQ8), and a particular HLA-DQ6 molecule (HLA-DQA1*0102–DQB1*0602) is associated with dominant protection from the disease. There is evidence that certain residues important for structure and function of both HLA-DQ and DR peptide-binding pockets determine disease susceptibility and resistance. Independent confirmation of the IDDM2 locus on chromosome 11p15.5 has been achieved in both case-control and family-based studies, whereas associations with the other potential IDDM loci have not always been replicated. Several possibilities to explain these variable results from different studies are discussed, and a key factor affecting both linkage and association studies is that the genetic basis of T1D susceptibility may differ between ethnic groups. Some future strategies to address these problems are proposed. These include increasing the sample size in homogenous ethnic groups, high throughput genotyping and genomewide linkage disequilibrium (LD) mapping to establish disease associated ancestral haplotypes. Elucidation of the function of particular genes (‘functional genomics’) in the pathogenesis of T1D will be a most important element in future studies in this field, in addition to more sophisticated methods of statistical analyses.

Genetics of Type 1 Diabetes: What's Next?

The discovery of the association between HLA in the major histocompatibility complex (MHC) on chromosome 6p21 with type 1 diabetes, but not with type 2 diabetes, suggested that these disease entities were of different genetic background and pathogenesis. The discovery that some individuals with diabetes had autoantibodies in their blood provided additional evidence that type 1 diabetes had an autoimmune origin. Recently, increasing knowledge of the genome, coupled with rapidly improving genotyping technology and availability of increasingly large numbers of samples, has enabled statistically robust, systematic, genome-wide examinations for discovery of loci contributing to type 1 diabetes susceptibility, including within the MHC itself. Currently, there are over 50 non-HLA regions that significantly affect the risk for type 1 diabetes (http://www.t1dbase.org). Many of these regions contain interesting, but previously unrecognized, candidate genes. A few regions contain genes of unknown function or no known annotated genes, suggesting roles for long-distance gene regulatory effects, noncoding RNAs, or unknown mechanisms. Against a background of ever-improving knowledge of the genome, particularly its transcriptional regulation, and with massive advances in sequencing, specific genes, rather than regions that impinge upon type 1 diabetes risk, will be identified soon. Here we discuss follow-up strategies for genome-wide association (GWA) studies, causality of candidate genes, and genetic association in a bioinformatics approach with the anticipation that this knowledge will permit identification of the earliest events in type 1 diabetes etiology that could be targets for intervention or biomarkers for monitoring the effects and outcomes of potential therapeutic agents. The International Type 1 Diabetes Genetics Consortium (T1DGC) has established significant resources for the study of genetics of type 1 diabetes. These resources are available to the research community and provide a basis for future discovery in the transition from gene mapping to discovery of disease mechanisms. The T1DGC (http://www.t1dgc.org) is an …

On the pathogenesis of IDDM.

SummaryA model of the pathogenesis of insulin-dependent diabetes mellitus, i.e. the initial phase of beta-cell destruction, is proposed: in a cascade-like fashion efficient antigen presentation, unbalanced cytokine, secretion and poor beta-cell defence result in beta-cell destruction by toxic free radicals (O2− and nitric oxide) produced by the beta cells themselves. This entire process is under polygenetic control.

A Tumour Necrosis Factor Beta Gene Polymorphism in Relation to Monokine Secretion and Insulin-Dependent Diabetes Mellitus

HLA‐class III region genes may be associated with susceptibility to insulin‐dependent diabetes mellitus (IDDM). In this study an Ncol polymorphism of the tumour necrosis factor beta (TNF‐β) gene, which is positioned next lo the tumour necrosis factor alpha (TNF‐α) gene in the HLA class 111 region, was detected by restriction fragment length polymorphism (RFLP). This polymorphism has previously been reported lo be located in the TNF‐α gene. Caucasian HLA‐DR3.4 heterozygous IDDM patients (n=‐26) and DR‐matched healthy controls (n=19). as well as randomly selected IDDM patients (n = 27) and controls (n = 25) were studied. In addition four multiplex families (49 individuals) and eight HLA‐non‐identical sibpairs concordant for IDDM were analysed.

FUNCTIONAL ANALYSIS OF A NEW POLYMORPHISM IN THE HUMAN TNF ALPHA GENE PROMOTER

In this paper the functional relevance of a TNFA promoter polymorphism, a G/A polymorphic sequence at position -238, was tested by analysing its influence on TNF alpha production upon in vitro stimulation of monocytes from 78 healthy, unrelated individuals by lipopolysaccharide (LPS) or after allogenic stimulation in a panel of 32 healthy individuals. All TNFA-A positive individuals were either DR3 or DR7 positive, confirming the previously reported strong linkage disequilibrium of the TNFA-A allele with the two extended haplotypes (B18, F1C30, DR3) and (B57, SC61, DR7). No individuals homozygous for the TNFA-A allele were present in the panel. The mean level of TNF alpha production was not significantly different in TNFA-G/G homozygous and in TNFA-A/G heterozygous individuals after LPS stimulation of monocytes (P = 0.35) or after allogenic stimulation (P = 0.7). After LPS and allogenic stimulation DR3 positive individuals had a higher mean TNF production. This could not be further differentiated by typing for TNF -283.