Insulin VNTR allele-specific effect in type 1 diabetes depends on identity of untransmitted paternal allele. The IMDIAB Group

Genetic variations within the insulin gene region are associated with accelerated fetal growth

Size at birth has been proposed to be associated with the risk of type 2 diabetes and cardiovascular disease later in life. It is, however, unclear whether this association is attributed to an unfavorable intrauterine environment or to specific genotypes predisposing both altered fetal growth and common diseases in adult life. The aim of this study was to investigate the associations between the neonatal birth size and the genotypes of polymorphic loci within the insulin gene (INS) region, which is susceptible to diabetes mellitus. We analyzed the genotypes of two polymorphic loci; -23HphI and HUMTH01, in 520 pairs of normal Japanese mothers and their neonates, and compared with the somatoscopic characteristics at birth converted into standard deviation scores (SDS) according to sex, parity and gestational weeks at delivery. It was revealed that neonatal -23HphI T allele and HUMTH01 allele10, which are linked to the INS variable number of tandem repeats (VNTR) class III allele, were associated with increased weight, head circumstance, and length at birth. These associations confirmed that variation within the INS region, most probably at the INS-VNTR, influences fetal growth. Furthermore, the finding that the paternally transmitted -23HphI T allele was exclusively correlated with increased size at birth indicates the involvement of an imprinting mechanism. In conclusion, the INS-VNTR class III allele might accelerate fetal growth in a parent-specific manner.

The insulin gene in type 1 diabetes

Insulin is a key autoantigen in the autoimmune process leading to the development of type 1 diabetes. Recent studies in both humans and mice have shown that variation in the expression of the insulin gene, in the thymus rather than the pancreas, contributes to disease susceptibility by affecting self-tolerance to insulin. These findings have brought about a paradigm-shift in our understanding of self-tolerance and autoimmunity to molecules with tissue-restricted expression, which are often the target of autoimmune disease.

A note on the power to detect transmission distortion in parent-child trios via the transmission disequilibrium test

Transmission distortion refers to deviation from the normal 50:50 transmission of alleles from parents to offspring. Identification of genomic regions which undergo distortion is necessary for the correct interpretation of linkage and association studies, since tests of linkage using affected relative pairs and family based tests of association will yield spurious results in the presence of transmission distortion. With the increasing availability of genome-wide high density SNP data (e.g. from the International HapMap project), identification of these loci is now a real possibility. Here we present an analytical formula which demonstrates that the power to detect transmission distortion is a simple function of the number of heterozygous parents in the sample and the level of distortion at the locus. Our results indicate that whilst it will be possible to identify loci undergoing major levels of distortion using tens or hundreds of trios, large sample sizes in the order of tens of thousands of trios will be necessary to detect minor levels of distortion with appreciable power. The corollary is that genome-wide searches are unlikely to identify loci where the level of distortion is small, although they may serve to identify interesting regions worthy of follow up.

Heterogeneity of class I INS VNTR allele association with insulin secretion in obese children

On the basis of the near-complete linkage disequilibrium of the insulin variable number of tandem repeats ( INS VNTR) allele with the neighboring −23Hph1 A/T single-nucleotide polymorphism, previous studies have documented the association of class I (“short”) and class III (“long”) INS VNTR alleles with metabolic parameters, including circulating insulin levels. Using a new method to sequence class I alleles, we revisited this association in 346 obese children. Class I alleles are made of several types of repeats, whose repartition determines subclasses IC and ID. Fasting insulin was found to be higher in obese children with ID/ID genotypes (135 ± 12 pmol/l, n = 64) than with ID/IC or IC/IC genotypes (91 ± 5 pmol/l, n = 97, P = 0.0005). In response to oral glucose, peak insulin levels and insulin-to-glucose area under the curve ratios were higher in ID/ID (872 ± 122 pmol/l and 109 ± 15, respectively) than in ID/IC or IC/IC patients (586 ± 42 pmol/l and 76 ± 5, P = 0.02 and P = 0.04, respectively). Fasting and postglucose insulin levels were comparable in carriers of IC and of class III alleles. Our results support that the molecular structure of the VNTR allele, not only its overall length, is associated with variations of insulin secretion. ID/ID homozygosity appears responsible for the increased insulin levels previously attributed to the whole class I VNTR group. It will be important to test the ramifications of this observation for class I association with Type 1 (susceptibility) and Type 2 diabetes (protection).

Genes mediating environment interactions in type 1 diabetes

The relative risk of type 1 (autoimmune) diabetes mellitus for a sibling of an affected patient is fifteen times that of the general population, indicating a strong genetic contribution to the disease. Yet, the incidence of diabetes in most Western communities has doubled every fifteen years since the Second World War - a rate of increase that can only possibly be explained by a major etiological effect of environment. Here, the authors provide a selective review of risk factors identified to date. Recent reports of linkage of type 1 diabetes to genes encoding pathogen pattern recognition molecules, such as toll-like receptors, are discussed, providing a testable hypothesis regarding a mechanism by which genetic and environmental influences on disease progress are integrated.

CTLA-4 (CD152) and its involvement in autoimmune disease

Autoimmune diseases (AID) are inherited as complex genetic diseases. Different Autoimmune diseases have been found to cluster in families and are believed to share some common etiological factors. With the exception of major histocompatibility complex (MHC) genes contributing susceptibility to these diseases have been difficult to identify. CD152 has emerged as one such candidate unifying several autoimmune diseases. We here review the evidence that CD152 constitutes a general susceptibility factor for multiple autoimmune diseases and discuss how CD152 and other co-stimulatory pathways may contribute to autoimmune pathogenesis.

Paramutation: an encounter leaving a lasting impression

Paramutation is the result of heritable changes in gene expression that occur upon interaction between alleles. Whereas Mendelian rules, together with the concept of genetic transmission via the DNA sequence, can account for most inheritance in sexually propagating organisms, paramutation-like phenomena challenge the exclusiveness of Mendelian inheritance. Most paramutation-like phenomena have been observed in plants but there is increasing evidence for its occurrence in other organisms, including mammals. Our knowledge of the underlying mechanisms, which might involve RNA silencing, physical pairing of homologous chromosomal regions or both, is still limited. Here, we discuss the characteristics of different paramutation-like interactions in the light of arguments supporting each of these alternative mechanisms.

A mixed epigenetic/genetic model for oligogenic inheritance of autism with a limited role for UBE3A

The genetic contribution to autism is often attributed to the combined effects of many loci (ten or more). This conclusion is based in part on the much lower concordance for dizygotic (DZ) than for monozygotic (MZ) twins, and is consistent with the failure to find strong evidence for linkage in genome-wide studies. We propose that the twin data are compatible with oligogenic inheritance combined with a major, genetic or epigenetic, de novo component to the etiology. Based on evidence that maternal but not paternal duplications of chromosome 15q cause autism, we attempted to test the hypothesis that autism involves oligogenic inheritance (two or more loci) and that the Angelman gene (UBE3A), which encodes the E6-AP ubiquitin ligase, is one of the contributing genes. A search for epigenetic abnormalities led to the discovery of a tissue-specific differentially methylated region (DMR) downstream of the UBE3A coding exons, but the region was not abnormal in autism lymphoblasts or brain samples. Based on evidence for allele sharing in 15q among sib-pairs, abnormal DNA methylation at the 5'-CpG island of UBE3A in one of 17 autism brains, and decreased E6-AP protein in some autism brains, we propose a mixed epigenetic and genetic model for autism with both de novo and inherited contributions. The role of UBE3A may be quantitatively modest, but interacting proteins such as those ubiquitinated by UBE3A may be candidates for a larger role in an oligogenic model. A mixed epigenetic and genetic and mixed de novo and inherited (MEGDI) model could be relevant to other "complex disease traits".

DNA methylation affects meiotic trans-sensing, not meiotic silencing, in Neurospora

During the early stages of meiosis in Neurospora, the symmetry of homologous chromosomal regions is carefully evaluated by actively trans-sensing their identity. If a DNA region cannot be detected on the opposite homologous chromosome, then this lack of "sensing" activates meiotic silencing, a post-transcriptional gene silencing-like mechanism that silences all genes in the genome with homology to the loop of unpaired DNA, whether they are paired or unpaired. In this work, we genetically dissected the meiotic trans-sensing step from meiotic silencing by demonstrating that DNA methylation affects sensing without interfering with silencing. We also determined that DNA sequence is an important parameter considered during meiotic trans-sensing. Altogether, these observations assign a previously undescribed role for DNA methylation in meiosis and, on the basis of studies in other systems, we speculate the existence of an intimate connection among meiotic trans-sensing, meiotic silencing, and meiotic recombination.

Neo-Lamarckian medicine

Darwinian medicine is the treatment of disease based on evolution. The underlying assumption of Darwinian medicine is that traits are coded by genes, which are often assumed to be sequences of DNA nucleotides. The quantitative genetic ramification of this perspective is that traits, including disease susceptibility, are either caused by genes or by the environment, with genotype-by-environment interactions usually considered statistical artefacts. I emphasize also examining those epigenetic signals that can be altered by environmental perturbations and then transmitted to subsequent generations. Although seldom studied, environmentally-alterable meiotically-heritable epigenetic signals exist and provide a mechanism underlying genotype-by-environment interactions. Environment of a parent can affect its descendants by heritably altering epigenetic signals. Neo-Lamarckian medicine is the application of these evolutionary epigenetic notions to diseases and could have enormous public health and environmental policy implications. If industrial contaminants adversely affect organisms by meiotically-heritably altering their epigenetic signals, then cleaning up these contaminants will not remedy the problem. Once contaminants have adversely altered an individual's epigenetic signals, this harm will be transmitted to future generations even if they are not exposed to the contaminant. Exposure to environmental shocks such as free radicals or other carcinogens can alter cytosine methylation patterns on regulatory genes. This can cause cancer by up-regulating genes for cell division or by down-regulating tumour suppressor genes. Environmentally-alterable meiotically-heritable epigenetic signals could also underlie other diseases, such as diabetes, Prader-Willi syndrome, and many complex diseases. If environmentally-altered meiotically-heritable epigenetic effects are widespread - which is an important open empirical question - they have the potential to alter paradigmatic views of evolutionary medicine and the putative dichotomy of nature versus nurture. Neo-Lamarckian medicine would thereby shift emphasis from cure to prevention of diseases.

Remapping the insulin gene/IDDM2 locus in type 1 diabetes

Type 1 diabetes susceptibility at the IDDM2 locus was previously mapped to a variable number tandem repeat (VNTR) 5' of the insulin gene (INS). However, the observation of associated markers outside a 4.1-kb interval, previously considered to define the limits of IDDM2 association, raised the possibility that the VNTR association might result from linkage disequilibrium (LD) with an unknown polymorphism. We therefore identified a total of 177 polymorphisms and obtained genotypes for 75 of these in up to 434 pedigrees. We found that, whereas disease susceptibility did map to within the 4.1-kb region, there were two equally likely candidates for the causal variant, -23HphI and +1140A/C, in addition to the VNTR. Further analyses in 2,960 pedigrees did not support the difference in association between VNTR lineages that had previously enabled the exclusion of these two polymorphisms. Therefore, we were unable to rule out -23HphI and +1140A/C having an etiological effect. Our mapping results using robust regression methods show how precisely a variant for a common disease can be mapped, even within a region of strong LD, and specifically that IDDM2 maps to one or more of three common variants in a approximately 2-kb region of chromosome 11p15.

Evidence for a Type 1 diabetes-specific mechanism for the insulin gene-associated IDDM2 locus rather than a general influence on autoimmunity

AIMS

The Type 1 diabetes susceptibility locus, IDDM2, has been mapped to a variable number of tandem repeats (VNTR) region 5' upstream of the insulin (INS) and insulin-like growth factor (IGF2) genes on chromosome 11p15. The function of the VNTR is uncertain; however, it may influence the thymic expression of the insulin gene and affect the development of immune self-tolerance. The aim of this study was to investigate whether the INS VNTR region is a Type 1 diabetes-specific locus or acting as a general autoimmunity gene.

METHODS

We genotyped the INS-IGF2 VNTR [using the surrogate INS-23 HphI single nucleotide polymorphism (SNP)] in 823 Graves' disease (GD)/multiple sclerosis (MS) families, 1433 GD/MS patients and 837 healthy control subjects.

RESULTS

We found no evidence of excess transmission of the allele associated with Type 1 diabetes to individuals affected by GD or MS within the families. Analysis of the case-control dataset showed no genotypic or allelic difference between the two populations.

CONCLUSIONS

These data suggest that the INS-IGF2 VNTR is acting as a Type 1 diabetes-specific susceptibility gene rather than as an influence on general autoimmunity.

5'-Insulin gene VNTR polymorphism is specific for type 1 diabetes: no association with celiac or Addison's disease

The VNTR region located at the 5'-end of the insulin gene on chromosome 11p15.5 is linked to susceptibility to type 1 diabetes mellitus (T1DM), and class I alleles have been associated with increased risk of disease, whereas class III alleles are considered to be protective. Although a potential effect on the expression level of thymic insulin and a consequent abnormal tolerance have been proposed as an explanation, it is still not clear whether the association is specific for T1DM or whether it is shared by other autoimmune disorders. To investigate the contribution of INS-VNTR to the genetic susceptibility to autoimmune disorders, we analyzed 102 autoantibody-positive T1DM patients, 59 patients with celiac disease (CD), and 57 patients with Addison's disease (ADD), as well as 111 unrelated healthy individuals from the general population. When analyzing the results, class I allele frequencies were 85.8% in the T1DM group, 77% among CD patients, 71% in the ADD group, and 76.1% in the general population. Association with increased risk was seen only in the T1DM group (pc = 0.015). Risk to T1DM was associated with the class I/class I homozygous genotype (RR, 1.92; 95% CI, 1.03-3.6). In conclusion, INS-VNTR does not seem to be involved in the susceptibility to autoimmune diseases other than T1DM and can be considered a diabetes-specific locus.

Natural Selection and the Evolution of Genome Imprinting

Sexual reproduction results from the fusion of gametes in which the chromatin configuration of maternal and paternal chromosomes is distinct at fertilization. Although many of the differences are erased during successive cellular divisions and chromatin modifications, some are retained in both somatic and germline cells. These epigenetic modifications can confer different characteristics on maternal and paternal chromosomes and such differences can be selected during any process that has the ability to distinguish between homologues. The end result of these selective forces are parental origin effects, writ large. The range of effects observed, including transcriptional imprinting and effects on chromosome segregation and heterochromatization, reflects the diversity of selective forces in operation. However, a closer look at these effects suggests that parental origin-dependent differences in chromatin structure might be subject to some common forces and that these forces may explain many of the "nontranscriptional" parental origin effects observed in mammals.

Epigenetics and bipolar disorder: New opportunities and challenges

Despite significant effort, understanding of the molecular causes and mechanisms of bipolar disorder (BD) remains a major challenge. Numerous molecular genetic linkage and association studies have been conducted over the last two decades; however, the data are quite inconsistent or even controversial. This article develops an argument that molecular studies of BD would benefit significantly from adding an epigenetic (epiG) perspective. EpiG factors refer to modifications of DNA and chromatin that "orchestrate" the activity of the genome, including regulation of gene expression. EpiG mechanisms are consistent with various non-Mendelian features of BD such as the relatively high degree of discordance in monozygotic (MZ) twins, the critical age group for susceptibility to the disease, clinical differences in males and females, and fluctuation of the disease course, including interchanges of manic and depressive phases, among others. Apart from the phenomenological consistency, molecular epiG peculiarities may shed new light on the understanding of controversial molecular genetic findings. The relevance of epigenetics for the molecular studies of BD is demonstrated using the examples of genetic studies of BD on chromosome 11p and the X chromosome. A spectrum of epiG mechanisms such as genomic imprinting, tissue-specific effects, paramutagenesis, and epiG polymorphism, as well as epiG regulation of X chromosome inactivation, is introduced. All this serves the goal of demonstrating that epiG factors cannot be ignored anymore in complex phenotypes such as BD, and systematic large-scale epiG studies of BD have to be initiated.

No evidence of type 1 diabetes susceptibility genes in the region centromeric of the HLA complex

There is strong evidence that DQB1, DQA1, and DRB1 alleles are not the only contributors to the human leukocyte antigen (HLA) linked type 1 diabetes (T1D) predisposition. Although the HLA complex is much studied for disease association, little is known about the neighboring centromeric region. We have previously found suggestive association on DQ2-DR3 haplotypes for marker D6S291, located 3.6-Mb centromeric of HLA-DQB1. This region on human chromosome 6 is syntenic to a part of the region adjacent to the mouse major histocompatibility complex (MHC) on chromosome 17, which has been suggested to harbor a susceptibility gene in mouse (Idd16). To evaluate a possible role of the region centromeric of HLA-DQB1 in human T1D, we have scanned the region with nine microsatellite markers in 267 T1D families from five different populations. Our results indicate that the characteristic strong linkage disequilibrium in the HLA complex does not extend into this region. Furthermore, we did not detect any consistent T1D association for the markers analyzed in the study. In conclusion, our data argue against the presence of any strong genetic susceptibility factors for T1D in the region centromeric of the HLA complex.

The genetics of autoimmune endocrine disease

The common autoimmune endocrinopathies result from an interaction between environmental factors and genetic predisposition. Several chromosomal gene regions have been shown to contribute to more than one disease, supporting the clinical observation that the autoimmune endocrine diseases cluster within individuals and families. Genetic studies have implicated the major histocompatability complex (MHC)-human leucocyte antigen (HLA) genes on chromosome 6p21, although this chromosomal region does not explain all of the genetic contribution to the various disorders. Non-MHC-HLA genes, including disease-specific loci, are beginning to be identified and the publication of the draft sequence of the human genome will undoubtedly expediate future discoveries. Combined with the establishment of large cohorts of subjects with disease and the development of technology capable of performing high-throughput genotyping, genetic studies are likely to impact on the future treatment and prevention of the common autoimmune endocrine diseases.

Trans allele methylation and paramutation-like effects in mice

In mammals, imprinted genes have parent-of-origin-specific patterns of DNA methylation that cause allele-specific expression. At Rasgrf1 (encoding RAS protein-specific guanine nucleotide-releasing factor 1), a repeated DNA element is needed to establish methylation and expression of the active paternal allele. At Igf2r (encoding insulin-like growth factor 2 receptor), a sequence called region 2 is needed for methylation of the active maternal allele. Here we show that replacing the Rasgrf1 repeats on the paternal allele with region 2 allows both methylation and expression of the paternal copy of Rasgrf1, indicating that sequences that control methylation can function ectopically. Paternal transmission of the mutated allele also induced methylation and expression in trans of the normally unmethylated and silent wild-type maternal allele. Once activated, the wild-type maternal Rasgrf1 allele maintained its activated state in the next generation independently of the paternal allele. These results recapitulate in mice several features in common with paramutation described in plants.

Genetic epidemiology of type 1 diabetes

Family and twin studies indicate that a substantial fraction of susceptibility to type 1 diabetes is attributable to genetic factors. These and other epidemiologic studies also implicate environmental factors as important triggers. Although the specific environmental factors that contribute to immune-mediated diabetes remain unknown, several of the relevant genetic factors have been identified using two main approaches: genome-wide linkage analysis and candidate gene association studies. This article reviews the epidemiology of type 1 diabetes, the relative merits of linkage and association studies, and the results achieved so far using these two approaches. Prospects for the future of type 1 diabetes genetics research are considered.

HLA associations in type 1 diabetes: DPB1 alleles may act as markers of other HLA-complex susceptibility genes

Alleles at the HLA-DQB1, -DQA1 and -DRB1 loci are major determinants for susceptibility to develop type 1 diabetes (T1D). Increasing evidence supports that also other genes in, or near, the HLA complex contribute to the HLA-encoded risk. Alleles at the DPB1 locus have been suggested to directly influence the risk conferred by DQB1, DQA1 and DRB1 alleles, but the results are conflicting. We therefore genotyped 217 families from Norway, Denmark, Sweden and southern France to address the role of DPB1 alleles in T1D. After taking into account linkage disequilibrium (LD) with DQB1, DQA1 and DRB1 alleles, we found evidence that some DPB1 alleles are associated with modulating the risk of developing T1D. However, we show that the strong LD in the HLA complex, and the presence of extended haplotypes complicate the interpretation of the results. On DQ2-DR3 haplotypes, both allele 3 at microsatellite D6S2223 located 5.3-Mb telomeric of DPB1 and the extended DQ2-DR3-B18 haplotype display much stronger association than DPB1 alleles. When we exclude these effects, most of the apparent association of DPB1 alleles on DQ2-DR3 haplotypes disappear. Taken together, although we cannot completely rule out an effect of some DPB1 alleles, we propose that the statistically significant, albeit weak, DPB1 associations found are most likely the result of LD with another unidentified disease-susceptibility gene(s) in this region.

The unstable trinucleotide repeat story of major psychosis

New hopes for cloning susceptibility genes for schizophrenia and bipolar affective disorder followed the discovery of a novel type of DNA mutation, namely unstable DNA. One class of unstable DNA, trinucleotide repeat expansion, is the causal mutation in myotonic dystrophy, fragile X mental retardation, Huntington disease and a number of other rare Mendelian neurological disorders. This finding has led researchers in psychiatric genetics to search for unstable DNA sites as susceptibility factors for schizophrenia and bipolar affective disorder. Increased severity and decreased age at onset of disease in successive generations, known as genetic anticipation, was reported for undifferentiated psychiatric diseases and for myotonic dystrophy early in the twentieth century, but was initially dismissed as the consequence of ascertainment bias. Because unstable DNA was demonstrated to be a molecular substrate for genetic anticipation in the majority of trinucleotide repeat diseases including myotonic dystrophy, many recent studies looking for genetic anticipation have been performed for schizophrenia and bipolar affective disorder with surprisingly consistent positive results. These studies are reviewed, with particular emphasis placed on relevant sampling and statistical considerations, and concerns are raised regarding the interpretation of such studies. In parallel, molecular genetic investigations looking for evidence of trinucleotide repeat expansion in both schizophrenia and bipolar disorder are reviewed. Initial studies of genome-wide trinucleotide repeats using the repeat expansion detection technique suggested possible association of large CAG/CTG repeat tracts with schizophrenia and bipolar affective disorder. More recently, three loci have been identified that contain large, unstable CAG/CTG repeats that occur frequently in the population and seem to account for the majority of large products identified using the repeat expansion detection method. These repeats localize to an intron in transcription factor gene SEF2-1B at 18q21, a site named ERDA1 on 17q21 with no associated coding region, and the 3' end of a gene on 13q21, SCA8, that is believed to be responsible for a form of spinocerebellar ataxia. At present no strong evidence exists that large repeat alleles at either SEF2-1B or ERDA1 are involved in the etiology of schizophrenia or bipolar disorder. Preliminary evidence suggests that large repeat alleles at SCA8 that are non-penetrant for ataxia may be a susceptibility factor for major psychosis. A fourth, but much more infrequently unstable CAG/CTG repeat has been identified within the 5' untranslated region of the gene, MAB21L1, on 13q13. A fifth CAG/CTG repeat locus has been identified within the coding region of an ion transporter, KCNN3 (hSKCa3), on 1q21. Although neither large alleles nor instability have been observed at KCNN3, this repeat locus has been extensively analyzed in association and family studies of major psychosis, with conflicting findings. Studies of polyglutamine containing genes in major psychosis have also shown some intriguing results. These findings, reviewed here, suggest that, although a major role for unstable trinucleotides in psychosis is unlikely, involvement at a more modest level in a minority of cases cannot be excluded, and warrants further investigation.

Transgenerational inheritance of epigenetic states at the murine Axin(Fu) allele occurs after maternal and paternal transmission

Phenotypic variation that cannot be explained by genetic or environmental heterogeneity has intrigued geneticists for decades. The molecular basis of this phenomenon, however, is largely a mystery. Axin-fused (Axin(Fu)), first identified in 1937, is a classic example of a mammalian allele displaying extremely variable expression states. Here we demonstrate that the presence or absence of its characteristic phenotype, a kinked tail, correlates with differential DNA methylation at a retrotransposon within Axin(Fu) and identify mutant transcripts arising adjacent to the retrotransposon LTR that are likely to be causative of the phenotype. Furthermore, the epigenetic state at Axin(Fu) can be inherited transgenerationally after both maternal and paternal transmission. This is in contrast to epigenetic inheritance at the murine agouti-viable yellow (A(vy)) allele, which occurs through the female only. Unlike the egg, the sperm contributes very little (if any) cytoplasm to the zygote, and therefore paternal inheritance at Axin(Fu) argues against the possibility that the effects are due to cytoplasmic or metabolic influences. Consistent with the idea of transgenerational inheritance of epigenetic marks, we find that the methylation state of Axin(Fu) in mature sperm reflects the methylation state of the allele in the somatic tissue of the animal, suggesting that it does not undergo epigenetic reprogramming during gametogenesis. Finally, we show that epigenetic inheritance is influenced by strain background. These findings enable us to propose a model for transgenerational epigenetic inheritance in mammals.

Dopamine D4 receptor and tyrosine hydroxylase genes in bipolar disorder: evidence for a role of DRD4

The involvement of the mesocorticolimbic dopamine system in behaviors that are compromised in patients with mood disorder has led to the investigation of dopamine system genes as candidates for bipolar disorder. In particular, the functional VNTRs in the exon III of the dopamine D4 (DRD4) and in intron I of the tyrosine hydroxylase (TH) genes have been investigated in numerous association studies that have produced contrasting results. Likewise, linkage studies in multiplex bipolar families have shown both positive and negative results for markers in close proximity to DRD4 and TH on 11p15.5. We performed a linkage disequilibrium analysis of the DRD4 and TH VNTRs in a sample of 145 nuclear families comprised of DSM-IV bipolar probands and their biological parents. An excess of transmissions and non transmissions was observed for the DRD4 4- and 2-repeat alleles respectively. The biased transmission showed a parent of origin effect (POE) since it was derived almost exclusively from the maternal meiosis (4-repeat allele maternally transmitted 40 times vs 20 times non-transmitted; chi(2) = 6.667; df = 1; P = 0.009; while paternally transmitted 26 times vs 21 times non-transmitted; chi(2) = 0.531; df = 1; P = 0.46). The analysis of TH did not reveal biased transmission of intron I VNTR alleles. Although replication of our study is necessary, the fact that DRD4 exhibit POE and is located on 11p15.5, in close proximity to a cluster of imprinted genes, suggests that genomic imprinting may be operating in bipolar disorder.

Molecular aspects of type 1 diabetes

Type 1 diabetes is a T cell mediated autoimmune disease, characterised by the selective destruction of pancreatic beta cells, and susceptibility is determined by a combination of genetic and environmental factors. The environmental agents implicated include viruses and dietary factors, although none has yet been shown to be directly responsible for triggering beta cell autoimmunity. The genetic factors that influence disease risk have been subjected to more intensive study and two gene regions of major importance have been identified: the human leucocyte antigen locus and the insulin gene. This review will focus on the mechanisms by which these genes might influence the risk of developing type 1 diabetes.

Evidence of at least two type 1 diabetes susceptibility genes in the HLA complex distinct from HLA-DQB1, -DQA1 and -DRB1

Susceptibility to, and protection against development of type 1 diabetes (T1D) are primarily associated with the highly polymorphic exon 2 sequences of the HLA class II genes: DQB1, DQA1 and DRB1. However, several studies have also suggested that additional genes in the HLA complex influence T1D risk, albeit to a lesser degree than the class II genes. We have previously shown that allele 3 of microsatellite marker D6S2223, 4.9 Mb telomeric of DQ in the extended class I region, is associated with a reduction in risk conferred by the DQ2-DR3 haplotype. Here we replicate this finding in two populations from Sweden and France. We also show that markers in the HLA class II, III and centromeric class I regions contribute to the DQ2-DR3 associated risk of T1D, independently of linkage disequilibrium (LD) with both the DQ/DR genes and the D6S2223 associated gene. The associated marker alleles are carried on the DQ2-DR3-B18 haplotype in a region of strong LD. By haplotype mapping, we have located the most likely location for this second DQ2-DR3 haplotype-modifying locus to the 2.35 Mb region between HLA-DOB and marker D6S2702, located 970 kb telomeric of HLA-B.

The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences

Paramutation is an interaction between alleles that leads to a heritable change in the expression of one allele. In B'/B-I plants, B-I (high transcription) always changes to B' (low transcription). The new B' allele retains the low expression state in the next generation and paramutates B-I at a frequency of 100%. Comparisons of the structure and expression of B' with that of a closely related allele that does not participate in paramutation demonstrated that transcription from the same promoter-proximal sequences is not sufficient for paramutation. Fine-structure recombination mapping localized sequences required for B' expression and paramutation. The entire 110 kb upstream of the B' transcription start site was cloned and sequenced and the recombination breakpoints were determined for 12 recombinant alleles. Sequences required for expression and paramutation mapped to distinct regions, 8.5-49 kb and 93-106 kb upstream of the B' transcription start site, respectively. Sequencing and DNA blot analyses indicate that the B' region required for paramutation is mostly unique or low copy in the maize genome. These results represent the first example of long-distance regulatory elements in plants and demonstrate that paramutation is mediated by long-distance cis and trans interactions.

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.

Behavior, heredity, and diabetes in college alumnae

OBJECTIVE

Diabetes has been increasing in incidence and prevalence in the United States. Physical activity and exercise have been shown to lower the risk of noninsulin-dependent diabetes (NIDD), and family history and genetic factors are associated with both insulin-dependent diabetes (IDD) (type 1) and NIDD. The objective of this paper is to examine risk factors for diabetes in female college graduates as part of a study designed to determine the long-term health of former college athletes compared with nonathletes. The study was first conducted in 1981-1982, and a follow-up study was conducted in 1996-1997.

METHODS

The subjects for this paper are 3940 college alumnae (1945 former athletes and 1995 nonathletes), who participated in the follow-up study by responding to a self-administered questionnaire on medical history, health, family history, and behavioral practices.

RESULTS

About 1.3% of the women reported physician-diagnosed diabetes, 0.9% of the former athletes, and 1.7% of the nonathletes. Former athletes had a significantly lower risk of NIDD, with an age-adjusted odds ratio (OR) of 0.41, 95% confidence level (CL) 0.2, 0.9. IDD was associated with a history of paternal diabetes (OR = 4.7, 95% CL 1.5, 14.9) and also with a history of diabetes in siblings (OR = 6.7, 95% CL 1.5, 30.1). NIDD was associated with a history of maternal diabetes (OR = 8.0, 95% CL 3.6, 17.8). Behavioral factors showed no association with IDD but were inversely associated with NIDD. The OR for being an athlete was 0.4, 95% CL 0.2, 0.9; for current regular exercise, OR = 0.4, 95% CL 0.2, 0.9; low body mass index (BMI) compared to high BMI, OR = 0.2, 95% CL 0.05, 0.60.

CONCLUSIONS

The findings that IDD is associated with paternal diabetes and that NIDD may be maternally transmitted are not widely known, although the mode of transmission of diabetes is receiving increasing attention in the medical and genetic literature. This study confirms that modifiable behavioral practices, such as physical activity and weight control (i.e., optimal BMI), reduce the risk of NIDD.

Genetics of osteoporosis: role of steroid hormone receptor gene polymorphisms

Osteoporosis is a common skeletal disease characterized by low bone mass and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility and susceptibility to fracture. In the past years, twin and family study have shown that this disease recognizes a strong genetic component and that genetic factors play an important role in regulating bone mineral density (BMD). While in few isolate conditions osteoporosis can be inherited in a simple Mendelian pattern, due to single gene mutations, in the majority of cases has to be considered a multifactorial polygenic disease in which genetic determinants are modulated by hormonal, environmental and nutritional factors. Given the important role that steroid hormones play in bone cell development and in the maintenance of normal bone architecture, polymorphisms at receptor of the steroid/thyroid hormone receptor superfamily, such as estrogen receptor alpha (ERalpha) and Vitamin D receptor (VDR) have been thoroughly investigated in the last years and appeared to represent important candidate genes. The individual contribution of these genetic polymorphisms to the pathogenesis of osteoporosis remains to be universally confirmed and an important aim in future work will be to define their functional molecular consequences and how these polymorphisms interact with each other and with the environment to cause the osteoporotic phenotype. A further promising application of genetic studies in osteoporosis comes from their pharmacogenomic implications, with the possibility to give a better guidance for therapeutic agents commonly used to treat this invalidating disorder or to identify target molecules for new therapeutic agents.

The insulin gene in diabetes

Lack of insulin production or abnormalities affecting insulin secretion are key to the development of almost all forms of diabetes, including the common type 1 (insulin-dependent) and type 2 (non-insulin-dependent) diabetes and the more rare forms of maturity-onset diabetes of the young (MODY). Because insulin has such a central role in the pathogenesis of both forms of diabetes, the insulin gene (INS) has always been considered a candidate susceptibility gene. A number of studies have shown that the allelic variation and parent-of-origin effects affect the transmission and expression of the insulin gene in pancreatic beta-cells and extra-pancreatic tissues. These observations have led to the formulation of new hypotheses to explain the biological mechanisms by which functional differences in the expression of the insulin gene may contribute to diabetes susceptibility.

Distinct and overlapping functions of insulin and IGF-I receptors

Targeted gene mutations have established distinct, yet overlapping, developmental roles for receptors of the insulin/IGF family. IGF-I receptor mediates IGF-I and IGF-II action on prenatal growth and IGF-I action on postnatal growth. Insulin receptor mediates prenatal growth in response to IGF-II and postnatal metabolism in response to insulin. In rodents, unlike humans, insulin does not participate in embryonic growth until late gestation. The ability of the insulin receptor to act as a bona fide IGF-II-dependent growth promoter is underscored by its rescue of double knockout Igf1r/Igf2r mice. Thus, IGF-II is a true bifunctional ligand that is able to stimulate both insulin and IGF-I receptor signaling, although with different potencies. In contrast, the IGF-II/cation-independent mannose-6-phosphate receptor regulates IGF-II clearance. The growth retardation of mice lacking IGF-I and/or insulin receptors is due to reduced cell number, resulting from decreased proliferation. Evidence from genetically engineered mice does not support the view that insulin and IGF receptors promote cellular differentiation in vivo or that they are required for early embryonic development. The phenotypes of insulin receptor gene mutations in humans and in mice indicate important differences between the developmental roles of insulin and its receptor in the two species.

The genetics of complex autoimmune diseases: non-MHC susceptibility genes

Susceptibility to complex autoimmune diseases (AIDs) is a multigenic phenotype affected by a variety of genetic and environmental or stochastic factors. After over a decade of linkage analyses, the identification of non-major histocompatibility complex (non-MHC) susceptibility alleles has proved to be difficult, predominantly because of extensive genetic heterogeneity and possible epistatic interactions among the multiple genes required for disease development. Despite these difficulties, progress has been made in elucidating the genetic mechanisms that influence the inheritance of susceptibility, and the pace of gene discovery is accelerating. An intriguing new finding has been the colocalization of several AID susceptibility genes in both rodent models and human linkage studies. This may indicate that several susceptibility alleles affect multiple AIDs, or alternatively that genomic organization has resulted in the clustering of many immune system genes. The completion of the human genome sequence, coupled with the imminent completion of the mouse genome, should yield key information that will dramatically enhance the rate of gene discovery in complex conditions such as AID susceptibility.

Genetics of type 1 diabetes

Type 1 diabetes mellitus is a T-cell-mediated autoimmune disease characterized by the selective destruction of pancreatic beta cells. Susceptibility to the disease is determined by a combination of genetic and environmental factors. The genetic factors are termed 'susceptibility genes' as they modify the risk of diabetes but are neither necessary nor sufficient for disease to develop. A large number of chromosomal regions have been identified as containing potential diabetes susceptibility genes. The IDDM1 locus, which encompasses the major histocompatibility complex on chromosome 6, is the major genetic risk factor. The HLA-DQ genes are the primary susceptibility genes within this region, although other genes may also contribute. The IDDM2 locus maps to a variable number of tandem repeats in the insulin gene region on chromosome 11. Further research is necessary to determine the precise location and identity of other diabetes susceptibility genes.

CTLA4 gene polymorphism contributes to the mode of onset of diabetes with antiglutamic acid decarboxylase antibody in Japanese patients: genetic analysis of diabetic patients with antiglutamic acid decarboxylase antibody

AIM

The mode of onset is occasionally similar in Type 1 and Type 2 diabetes mellitus, and some patients with Type 2 diabetes are positive for antiglutamic acid decarboxylase antibody (GAD Ab). We investigated the contribution of Type 1 diabetes susceptibility genes to the progression of the insulin-deficient state and mode of onset of Type 2 diabetes in GAD Ab-positive (GAD-Ab+) patients. We examined the variable number of tandem repeats in the promoter region of the insulin gene (INS-VNTR, insulin-dependent diabetes mellitus (IDDM) 2) and cytotoxic T lymphocyte antigen 4 (CTLA4, IDDM12) as representative of Type 1 diabetes susceptibility genes.

METHODS

Patients with Type 2 diabetes who were GAD-Ab+ (n = 51) were selected for this study. In INS-VNTR, the class I allele was classified according to length (1S, 25-38 repeat units; 1M, 39-41 repeat units; 1L, 42-44 repeat units) and the exact class I allele length was analysed by specific polymerase chain reaction (PCR) amplifications. Analyses of classes II and III were performed by Southern blot. CTLA4 gene polymorphism (exon 1 position 49, G/A) was analysed by PCR-restriction fragment length polymorphism.

RESULTS

The distribution of INS-VNTR was no different between Type 1 diabetes and Type 2 diabetes with GAD Ab. The allele frequencies of CTLA4 gene polymorphism G and A in Type 2 diabetes/GAD-Ab+ were significantly different from those of Type 1 diabetes/GAD-Ab+ (G: 53%, A: 47% vs. G: 84%, A: 16%; P < 0.0001).

CONCLUSIONS

Our data showed that GAD-Ab+ Japanese patients presenting with Type 2 diabetes have shifted A allele while patients with abrupt onset have shifted G allele of CTLA4 gene polymorphism. Our results suggest that immunological function and polymorphism of the CTLA4 gene may contribute to the pathogenesis and progression of Type 1 diabetes.

No evidence for SEL1L as a candidate gene for IDDM11-conferred susceptibility

BACKGROUND

The SEL1L gene is located on human chromosome 14q24.3-31 close to D14S67 which has been previously proposed to be a type 1 diabetes mellitus locus (IDDM11). Sel-1 is a negative regulator of the Notch signalling pathway and SEL1L is selectively expressed in adult pancreas and islets of Langerhans. This suggests that SEL1L may be a candidate gene for IDDM11.

METHODS

We have analysed two newly identified CA-repeat polymorphisms within the genomic sequence of the SEL1L locus for association with type 1 diabetes mellitus (T1DM) in 152 Danish T1DM-affected sib-pair families and in 240 Sardinian families (229 simplex and 11 sib-pair families).

RESULTS

No evidence for association of the two SEL1L markers with T1DM was observed in either the Danish or the Sardinian families. We have also used allelic sharing methods to analyse linkage with T1DM in the IDDM11 region using the same markers and the Danish collection of affected sib-pair families. No evidence of linkage was observed (Z(max)=0.86).

CONCLUSION

Although several lines of evidence suggest that SEL1L might be a candidate for IDDM11-conferred susceptibility to T1DM the present study does not support this hypothesis.

Risk assessment, prediction and prevention of type 1 diabetes

Circulating antibodies to pancreatic beta-cell antigens are markers of islet autoimmunity. In first-degree relatives of persons with type 1 diabetes, the levels and range of antigen specificities of these islet antibodies reflect the risk for clinical diabetes. However, in the general population, in which the disease prevalence is up to 30-fold lower, the predictive value of islet antibodies is correspondingly less. Islet antibody assays are primarily research tools to identify 'prediabetic' individuals for secondary prevention trials, but can also discriminate type 1 diabetes in several clinical situations. Loss of first-phase insulin response (FPIR) to intravenous glucose signifies imminent diabetes, but FPIR is normal in most islet-antibody-positive individuals. The contribution of a single FPIR measurement to risk assessment is therefore limited, but rate of fall of FPIR may be a useful predictor. Although beta cells are destroyed by autoreactive T cells, the assay of islet antigen-reactive T cells is not routine. Genetically, the major histocompatibility complex encoding human leukocyte antigen (HLA) alleles accounts for about 50% of familial clustering of type 1 diabetes. HLA typing is not diagnostic, but can be used to differentiate high- from low-risk individuals, e.g. at birth. While 'preclinical' diagnosis raises important medical and ethical questions, an optimized screening strategy provides a basis for counselling and follow-up. Recent knowledge of disease mechanisms and 'proof-of-principle' in the non-obese diabetic (NOD) mouse model justify expectations that type 1 diabetes is preventable, and even intervention that only delays onset of clinical diabetes is likely to be cost-effective.

The marks, mechanisms and memory of epigenetic states in mammals

It is well recognized that there is a surprising degree of phenotypic variation among genetically identical individuals, even when the environmental influences, in the strict sense of the word, are identical. Genetic textbooks acknowledge this fact and use different terms, such as 'intangible variation' or 'developmental noise', to describe it. We believe that this intangible variation results from the stochastic establishment of epigenetic modifications to the DNA nucleotide sequence. These modifications, which may involve cytosine methylation and chromatin remodelling, result in alterations in gene expression which, in turn, affects the phenotype of the organism. Recent evidence, from our work and that of others in mice, suggests that these epigenetic modifications, which in the past were thought to be cleared and reset on passage through the germline, may sometimes be inherited to the next generation. This is termed epigenetic inheritance, and while this process has been well recognized in plants, the recent findings in mice force us to consider the implications of this type of inheritance in mammals. At this stage we do not know how extensive this phenomenon is in humans, but it may well turn out to be the explanation for some diseases which appear to be sporadic or show only weak genetic linkage.

Above and within the genome: epigenetics past and present

Epigenetic regulation involves the maintenance of a particular state of gene expression--most commonly, repression--in the face of repeated mitosis, and frequently meiosis. Remarkably, changes in such heritable expression states occur without an alteration of the primary DNA sequence. We present a brief history of research in epigenetics, beginning with pioneering work in the 1950s by B. McClintock and R. A. Brink on maize kernel color inheritance. We describe the complex biochemistry of DNA methylation--the molecular basis of most epigenetic regulation in mammalian genomes--and review data connecting it to targeted modification and remodeling of chromatin structure. Several prominent examples of epigenetically regulated loci--X chromosome inactivation, imprinting, repetitive DNA silencing, and aberrant methylation patterns in neoplasia--are reviewed along with a description of our current understanding of the underlying molecular mechanisms. A common theme that emerges is the complex integration of epigenetic regulatory pathways with the chromatin infrastructure over target DNA loci.

Association study designs for complex diseases

Assessing the association between DNA variants and disease has been used widely to identify regions of the genome and candidate genes that contribute to disease. However, there are numerous examples of associations that cannot be replicated, which has led to skepticism about the utility of the approach for common conditions. With the discovery of massive numbers of genetic markers and the development of better tools for genotyping, association studies will inevitably proliferate. Now is the time to consider critically the design of such studies, to avoid the mistakes of the past and to maximize their potential to identify new components of disease.

Estrogen receptor alpha gene polymorphisms and bone mineral density: haplotype analysis in women from the United Kingdom

Genetic factors are important in the pathogenesis of osteoporosis and the estrogen receptor has been suggested as a possible candidate gene for regulation of bone mineral density (BMD). We investigated the relationship between PvuII, XbaI, and dinucleotide (TA)n repeat polymorphisms of the estrogen receptor alpha (ER-alpha) gene and BMD in a study of women from northeast Scotland in the United Kingdom. No significant association was observed between BMD values at the lumbar spine (LS) and femoral neck (FN) in relation to PvuII and XbaI polymorphisms individually, but haplotype analysis showed that BMD values (Z score) were significantly lower in those who carried the Px haplotype (n = 36) compared with those who did not (n = 170) at both the LS (mean +/- SEM; -0.775 +/- 0.125 vs. -0.285 +/- 0.082;p = 0.002) and the FN (-0.888 +/- 0.130 vs. -0.335 +/- 0.083; p = 0.0006). In keeping with this, the Px haplotype also was found to be an independent predictor of LS BMD (p = 0.019) and FN BMD (p = 0.005) in a multiple regression analysis model that included other possible predictors of BMD including age, years since menopause (YSM), hormone-replacement therapy (HRT) use, weight, and height. This model explained 15.7% and 23.4% of the total observed variance in LS and FN BMD, respectively, with the Px haplotype accounting for approximately 3% of the variance at both sites. Although the TA repeat polymorphism was in strong linkage disequilibrium (LD) with the PvuII (chi2 = 109.8; p < 0.0001) and XbaI (chi2 = 97.2; p < 0.0001) polymorphisms, there was no overall association between TA repeat number and BMD. We conclude that polymorphisms of the ER-alpha gene are significantly related to BMD in our population and that this association is dependent on the Px haplotype, suggesting that it is the Px haplotype, or a linked polymorphism, that confers risk.

Natural selection and the function of genome imprinting: beyond the silenced minority

Most hypotheses of the evolutionary origin of genome imprinting assume that the biochemical character on which natural selection has operated is the expression of the allele from only one parent at an affected locus. We propose an alternative - that natural selection has operated on differences in the chromatin structure of maternal and paternal chromosomes to facilitate pairing during meiosis and to maintain the distinction between homologues during DNA repair and recombination in both meiotic and mitotic cells. Maintenance of differences in chromatin structure in somatic cells can sometimes result in the transcription of only one allele at a locus. This pattern of transcription might be selected, in some instances, for reasons that are unrelated to the original establishment of the imprint. Differences in the chromatin structure of homologous chromosomes might facilitate pairing and recombination during meiosis, but some such differences could also result in non-random segregation of chromosomes, leading to parental-origin-dependent transmission ratio distortion. This hypothesis unites two broad classes of parental origin effects under a single selective force and identifies a single substrate through which Mendel's first and second laws might be violated.