Identification of novel alleles at a polymorphic microsatellite repeat region in the human NRAMP1 gene promoter: analysis of allele frequencies in primary biliary cirrhosis

Genetics and epigenetics in the pathogenesis of primary biliary cholangitis

Primary biliary cholangitis (PBC) is a chronic, slowly progressive cholestatic autoimmune liver disease predominantly afflicting women. PBC is characterized by the presence of disease-specific antimitochondrial antibodies and the histological destruction of intrahepatic bile ducts, which eventually lead to cirrhosis and hepatic failure. Fortunately, ursodeoxycholic acid therapy has improved the outcome of the vast majority of PBC cases. Although the etiology of PBC has not yet been elucidated, human leukocyte antigen (HLA) class II alleles have been consistently associated with disease onset for decades. PBC patients may also have genetically determined risk factors in non-HLA regions. Meanwhile, exposure to environmental factors, such as infectious diseases and harmful chemicals, can produce epigenetic alterations in some individuals and subsequent PBC onset. In this review, we describe the influence of HLA alleles and other gene polymorphisms on PBC along with the results of genome-wide association studies on this disease and its future prospects in terms of epigenetics.

Associations between NRAMP1 Polymorphisms and Susceptibility to Ulcerative Colitis/Crohn's Disease: A Meta-Analysis

OBJECTIVE

Multiple environmental and genetic factors contribute to the risks of ulcerative colitis (UC) and Crohn's disease (CD). Several allelic variants have been identified in natural resistance associated macrophage protein 1 (NRAMP1) gene; however, their association with UC/CD remains conflicting. The purpose of this study was to evaluate whether NRAMP1 polymorphisms are associated with the susceptibility to UC/CD.

METHODS

A meta-analysis on the association between the NRAMP1 polymorphisms and susceptibility to UC/CD was performed. Relevant studies were retrieved from the databases. After eligible data were extracted, Mantel-Haenszel statistics and random/fixed effects model were applied to calculate the pooled odds radio (OR) and 95% confidence interval (95% CI).

RESULTS

Seven articles containing 536 UC cases, 997 CD cases, and 1361 controls were collected. No significant association between allele 2 frequency of NRAMP1 and susceptibility to UC/CD was detected in overall population (all p > 0.05). However, increased UC/CD risk for allele 3 was observed in Caucasian population (OR = 1.27, 95% CI = 1.08~1.50, p = 0.04), whereas decreased UC/CD risk was detected in non-Caucasian population (OR = 0.72, 95% CI = 0.60~0.87, p < 0.001), under "allele 3 vs. other alleles" model. Moreover, a significant increase in CD risk for T carrier frequency of -237 C/T (OR = 0.44, 95% CI, 0.26~0.75, p = 0.003) was detected, but not 274 C/T and 1729+55del4 (TGTG) +/del.

CONCLUSIONS

The polymorphism of -237 C/T is related to the risk of CD; and the association of allele 3 with UC/CD risk differs in Caucasian and non-Caucasian population, which might be the potential biomarkers for clinical diagnosis of UC/CD.

Association of the solute carrier family 11 member 1 gene polymorphisms with susceptibility to leprosy in a Brazilian sample

Natural resistance-associated macrophage protein 1/solute carrier family 11 member 1 gene (Nramp1/Slc11a1) is a gene that controls the susceptibility of inbred mice to intracellular pathogens. Polymorphisms in the human Slc11a1/Nramp1 gene have been associated with host susceptibility to leprosy. This study has evaluated nine polymorphisms of the Slc11a1/Nramp1 gene [(GT)n, 274C/T, 469+14G/C, 577-18G/A, 823C/T, 1029 C/T, 1465-85G/A, 1703G/A, and 1729+55del4] in 86 leprosy patients (67 and 19 patients had the multibacillary and the paucibacillary clinical forms of the disease, respectively), and 239 healthy controls matched by age, gender, and ethnicity. The frequency of allele 2 of the (GT)n polymorphism was higher in leprosy patients [p = 0.04, odds ratio (OR) = 1.49], whereas the frequency of allele 3 was higher in the control group (p = 0.03; OR = 0.66). Patients carrying the 274T allele (p = 0.04; OR = 1.49) and TT homozygosis (p = 0.02; OR = 2.46), such as the 469+14C allele (p = 0.03; OR = 1.53) of the 274C/T and 469+14G/C polymorphisms, respectively, were more frequent in the leprosy group. The leprosy and control groups had similar frequency of the 577-18G/A, 823C/T, 1029C/T, 1465-85G/A, 1703G/A, and 1729+55del4 polymorphisms. The 274C/T polymorphism in exon 3 and the 469+14G/C polymorphism in intron 4 were associated with susceptibility to leprosy, while the allele 2 and 3 of the (GT)n polymorphism in the promoter region were associated with susceptibility and protection to leprosy, respectively.

Genome-Wide Association Studies in Primary Biliary Cirrhosis

Genome-wide association studies (GWASs) have been a significant technological advance in our ability to evaluate the genetic architecture of complex diseases such as primary biliary cirrhosis (PBC). To date, six large-scale studies have been performed that have identified 27 risk loci in addition to human leukocyte antigen (HLA) associated with PBC. The identified risk variants emphasize important disease concepts; namely, that disturbances in immunoregulatory pathways are important in the pathogenesis of PBC and that such perturbations are shared among a diverse number of autoimmune diseases-suggesting the risk architecture may confer a generalized propensity to autoimmunity not necessarily specific to PBC. Furthermore, the impact of non-HLA risk variants, particularly in genes involved with interleukin-12 signaling, and ethnic variation in conferring susceptibility to PBC have been highlighted. Although GWASs have been a critical stepping stone in understanding common genetic variation contributing to PBC, limitations pertaining to power, sample availability, and strong linkage disequilibrium across genes have left us with an incomplete understanding of the genetic underpinnings of disease pathogenesis. Future efforts to gain insight into this missing heritability, the genetic variation that contributes to important disease outcomes, and the functional consequences of associated variants will be critical if practical clinical translation is to be realized.

Herb-induced autoimmune-like hepatitis in C57BL/6J mice

BACKGROUND & AIMS

Animal model suitable for studying herb-induced experimental autoimmune hepatitis (AIH) remains a challenging problem. A medicinal herb containing Scutellaria baicalensis Georgi (Sb) and Bupleurum chinense DC (Bc) has been sporadically reported to be related to liver fibrosis. The aim of this study was to investigate the effects of Sb and Bc on experimental AIH in mice.

METHODS

C57BL/6J mice received intraperitoneal injection of Sb and/or Bc herbal extracts (1 mg/kg) for 4 or 8 weeks. Serum samples were collected to analyse serum transferase (AST, ALT), creatinine, markers for AIH and hepatic cytokine levels such as IFN-γ, IL10 and TGF-β1. Peripheral mononuclear cell (PBMC) gene expression profiles were analysed to show their effects on immune system.

RESULTS

Our results showed that Sb or Bc treatment increased serum AST, ALT, IgG and ANA levels. Prominent necroinflammatory changes were demonstrated in the livers of Sb- or Bc-treated mice while the decrease in IFN-γ and elevation of IL10 and TGF-β1 levels in liver tissues. Furthermore, the PMBC gene expression profile suggested that Sb or Bc treatment could modulate immune responses.

CONCLUSION

We conclude that the presence of AIH in Sb- or Bc-treated mice and C57BL/6J strain mice is a reliable animal model for studying herb-induced AIH-like hepatitis.

The role of vitamin d in primary biliary cirrhosis: possible genetic and cell signaling mechanisms

Primary biliary cirrhosis (PBC) is an immune-mediated chronic inflammatory disease of the liver of unknown etiology. Vitamin D deficiency is highly prevalent in patients with PBC, and many studies have demonstrated the significant effect of calcitriol on liver cell physiology. Vitamin D has antiproliferative and antifibrotic effects on liver fibrosis. Genetic studies have provided an opportunity to determine which proteins link vitamin D to PBC pathology (e.g., the major histocompatibility complex class II molecules, the vitamin D receptor, toll-like receptors, apolipoprotein E, Nramp1, and cytotoxic T lymphocyte antigen-4). Vitamin D also exerts its effect on PBC through cell signaling mechanisms, that is, matrix metalloproteinases, prostaglandins, reactive oxygen species, and the transforming growth factor betas. In conclusion, vitamin D may have a beneficial role in the treatment of PBC. The best form of vitamin D for use in the PBC is calcitriol because it is the active form of vitamin D3 metabolite, and its receptors are present in the sinusoidal endothelial cells, Kupffer cells, and stellate cells of normal livers, as well as in the biliary cell line.

Duplication of MER115 on chromosome 4 in patients with primary biliary cirrhosis

BACKGROUND

Primary biliary cirrhosis (PBC) is a complex disease with genetic and environmental influences. The disease is more prevalent in families with PBC and candidate gene case-control studies have linked PBC with DRB1(*)08 human leucocyte antigen class II alleles.

AIMS

The goal of this study was to characterize a MER115 intergenic region on chromosome 4 as a putative genetic variant associated with PBC.

METHODS/RESULTS

This region was incidentally identified during investigations to discover candidate microbial agents using representational difference analysis (RDA) with liver samples from patients with PBC and primary sclerosing cholangitis (PSC). blast search analysis of all the RDA products from the PBC liver revealed genomic sequences, whereas Escherichia coli, mycoplasma and hepatitis B virus DNA were found in the PSC liver. We identified one of the PBC RDA products as an ancestral repeat, referred to as MER115. Southern blot analysis with the PBC product uncovered a restriction fragment length polymorphism in PBC patients' liver. Southern blot hybridization signal showed increased signal intensity in PBC vs. control patients' DNA (P<0.005) and slot blot hybridization studies confirmed a copy number variation of the MER115 in hepatic DNA of PBC vs. control patients (P=0.02).

CONCLUSIONS

Further comparative genetic studies will be required to determine the extent of genomic duplication associated with MER115 and provide data on the possible copy number variants of genes close to this intergenic region in patients with PBC.

Genetic background of primary biliary cirrhosis

The clustering of patients in a representative family as well as relatively high concordance rate in monozygotic twins strongly indicate that genetic factors play a crucial role in modulating primary biliary cirrhosis (PBC) by conferring susceptibility to, or providing protection from, the disease. Therefore, much like other autoimmune diseases, intensive investigations have attempted to elucidate which genes are incriminated in the etiology of PBC. So far, a number of genes, including major histocompatibility complex (MHC) class I and II, cytokines and cell surface molecules, have been examined to seek the possibility of whether single nucleotide polymorphisms (SNP) of the gene might be associated with susceptibility to PBC. Nevertheless, it appears that methodologicaldifficulties, mainly the limitation of the number of individuals tested in each study, hamper the detection of a convincing and reproducible link between genetic polymorphisms and the etiology of PBC. Also, the difference in genetic background among several ethnic groups may play a role in concealing the association. In this review, I will highlight the genetic association in PBC, and review the association of genetic polymorphisms with the etiology of PBC, which have been reported in various ethnicities.

NRAMP1 (SLC11A1): A Plausible Candidate Gene for Systemic Sclerosis (SSc) with Interstitial Lung Involvement

Systemic sclerosis (SSc), also termed "scleroderma," is a progressive, systemic disease of unknown origin characterized by excessive fibrosis, vascular abnormalities and immune dysfunction. Nramp 1 gene has multiple pleiotropic effects on macrophage activation pathways, including up-regulation of the chemokine/cytokine genes KC, tumor necrosis factor alpha, interleukin-1 b, inducible nitric oxide syntase, and major histocompatibility complex class II expression, as well as tumoricial activity and antimicrobial activity. All of these pleiotropic effects are important for resistance to infection, but they may also be involved in the induction and maintenance of autoimmune diseases. We analyzed four natural resistance associated macrophage protein 1 (NRAMP1) gene polymorphisms including 5' promoter (GT)n microsatellite, INT4 (469 + 14G/C), 3'UTR (1729 + 55del4), and D543N (codon 543, Asp to Asn) in 52 systemic sclerosis patients with interstitial lung involvement and 136 healthy controls. We found a significant association between INT4, (GT)n polymorphisms (p = 0.006 and 0.027, respectively), and SSc. Our findings suggest that NRAMP1 is a plausible candidate gene for SSc.

Crohn's disease and SLC11A1 promoter polymorphism

Crohn's disease (CD) is a chronic multifactorial inflammatory disease. The prevalence of CD in Ashkenazi Jews is higher than in Sephardic Jews. SLC11A1, also known as Nramp1, is a divalent cation antiporter essential for the elimination of intraphagosomal pathogens. SLC11A1 has seven alleles in the promoter region and previous studies have suggested an association between CD and SLC11A1. The aim of this study was to check for a possible association between SLC11A1 promoter alleles and CD in Ashkenazi Jewish patients. DNA samples from healthy Ashkenazi donors and Ashkenazi CD patients were obtained and analyzed for SLC11A1 promoter polymorphism by PCR and DNA sequencing. One hundred thirty-one samples from healthy donors and 131 samples from CD patients were analyzed. Four alleles were identified: approximately 70% of the samples carried allele 3; approximately 30%, allele 2; approximately 1%, allele 1; and <1%, allele 5. There was no difference in allele frequencies between healthy donors and CD patients. No correlation was found between mutations in NOD2/CARD15 and the phenotype of CD. We conclude that the difference in SLC11A1 promoter polymorphism plays no role in CD in Ashkenazi Jews.

The -237C-->T promoter polymorphism of the SLC11A1 gene is associated with a protective effect in relation to inflammatory bowel disease in the South African population

The purpose of this study was to assess the likelihood that variation in the promoter region of the solute carrier family 11 member 1 gene (SLC11A1) contributes to inflammatory bowel disease (IBD) susceptibility in the South African population. The study cohort included 102 IBD patients, 47 with Crohn's disease (CD) and 55 with ulcerative colitis, and 192 population-matched controls. Mutation analysis revealed two novel alleles for the 5'-(GT)n repeat polymorphism, t(gt)5ac(gt)5ac(gt)6ggcaga(g)6 (allele 8) and t(gt)5ac(gt)5ac(gt)8ggcaga(g)6 (allele 9), and one previously documented point mutation -237C-->T. A significantly decreased frequency of the -237C-->T promoter polymorphism was observed in the patient group with IBD (p<0.001) and CD (p<0.0006) compared with the population-matched control group. These findings may be related to previous in vitro studies, which demonstrated that the point mutation at nucleotide position -237 represents a functional polymorphism that affects regulation of the upstream 5'-(GT)n repeat polymorphism differentially upon iron loading. Our findings raise the possibility that iron dysregulation mediated by allelic effects of SLC11A1 may contribute to IBD susceptibility.

Genes and (auto)immunity in primary biliary cirrhosis

Primary biliary cirrhosis (PBC) is a chronic autoimmune cholestatic liver disease most commonly encountered in postmenopausal women; it is characterized by high-titer serum autoantibodies to mitochondrial antigens, elevated serum IgM, progressive destruction of intrahepatic bile ducts, and ultimately liver cirrhosis and failure. The cytopathic mechanisms leading to the selective destruction of intrahepatic cholangiocytes are still largely unknown. The current theory on the pathogenesis of PBC indicated that environmental factors might trigger autoimmunity in genetically susceptible individuals. In fact, genetic predisposition is critical to disease onset and progression, yet peculiar among autoimmune diseases, as indicated by the lack of a strong association with major histocompatibility complex haplotypes. Further, the recently reported concordance rate among monozygotic twins strengthens the importance of genetic factors, while also indicating that additional factors, possibly infectious agents or xenobiotics, intervene to trigger the disease. In this review, the available data regarding the genetic factors associated with PBC susceptibility and progression, as well as the available evidence regarding the immunomediated pathogenesis of PBC, will be critically illustrated and discussed.

NRAMP1 is not associated with asthma, atopy, and serum immunoglobulin E levels in the French Canadian population

Reduced infection by mycobacteria, including Mycobacterium tuberculosis, may be partly responsible for increased prevalence of allergic and autoimmune diseases in developed countries. In a murine model of innate resistance to mycobacteria, the Nramp1 gene has been shown to affect asthma susceptibility. From this observation, it was proposed that human NRAMP1 may be a modulator of asthma risk in human populations. To experimentally test the candidacy of NRAMP1 in asthma susceptibility, we characterized five genetic variants of NRAMP1 (5'CAn, 274C>T, 469+14G>C, D543N, and 1729+del4) in an asthma family-based cohort from northeastern Quebec. We did not observe any significant association between NRAMP1 variants (either allele or haplotype specific) with asthma, atopy, or serum immunoglobulin E levels. These results demonstrate that, in spite of direct involvement of Nramp1 in a murine asthma model, in human populations NRAMP1 is not likely to be a major contributor to the genetic etiology of asthma and asthma-related phenotypes.

Association of functional polymorphisms of SLC11A1 with risk of esophageal cancer in the South African Colored population

Several environmental factors have been implicated in the etiology of esophageal cancer (EC). The purpose of this study was to assess the likelihood that variation in the SLC11A1 gene contributes to EC susceptibility, possibly due to its role in inflammation and iron metabolism. The regions of the gene containing potential functional polymorphisms, including the promoter region and exon 2, were investigated. The study cohort included 105 EC South African Colored patients with squamous cell carcinoma (SCC) and 110 population-matched controls, with South African Colored referring to individuals of mixed ancestry. A significantly decreased frequency of the -237C-->T promoter polymorphism was observed in the patient group with EC compared with the population-matched control group (P < 0.002, chi(2) with Yates's correction=7.87). A statistically significant disease association was also observed with allele 3 of the 5'-(GT)n promoter polymorphism (P < 0.0006, chi(2) with Yates's correction=10.16), but only in the absence of the T-allele at nucleotide position -237 following allelic stratification. Four novel variants were identified in intron 1 (IVS1-28C-->T) and exon 2 (112G-->A, 148delGACCAGCCC, 157insGACCAGCCCAG). The novel intronic polymorphism, IVS1-28C-->T, was also significantly associated with EC (P < 0.05, chi(2) with Yates's correction=2.52). We demonstrate association of genetic variation in both the promoter region and intron 1 of the SLC11A1 gene with EC susceptibility.

From bases to basis: linking genetics to causation in primary biliary cirrhosis

Primary biliary cirrhosis (PBC) is a multifactorial autoimmune disease with inherited and environmental components in pathogenesis. It is exceptional among autoimmune diseases in showing strong heritability according to familial occurrence and monozygotic twins concordance, yet with weak associations with the usual genetic risk elements for autoimmunity, such as the HLA alleles. Among the latter, there is risk (at least in some populations) conferred by HLA DRB1*08 and possibly some protection by DRB1*11. However, the inconsistency among studies on HLA is surprising, given that PBC is a relatively homogenous disease entity. Among non-HLA genes, some studies implicate polymorphisms of genes for cytotoxic T-lymphocyte antigen-4, interleukin-2, or interleukin-10; polymorphisms of the vitamin D receptor could synergize with low sunlight exposure to create deficiency of the immunoregulatory factor, activated vitamin D. A new lead is available from the finding in female subjects with PBC of an increase in the degree of monosomy of the X chromosome that is presumed to carry immune response genes. A further suggested source of inquiry is the apparent protection of African-American women from PBC. Finally, data on inheritance should be sought in PBC by descent methodology, rather than by cross-sectional association studies in cases and control subjects, and based on analysis of a large number of families with an affected member through a worldwide effort.

Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes

Background

One strategy to help identify susceptibility genes for complex, multifactorial diseases is to map disease loci in a representative animal model of the disorder. The nonobese diabetic (NOD) mouse is a model for human type 1 diabetes. Linkage and congenic strain analyses have identified several NOD mouse Idd (insulin dependent diabetes) loci, which have been mapped to small chromosome intervals, for which the orthologous regions in the human genome can be identified. Here, we have conducted re-sequencing and association analysis of six orthologous genes identified in NOD Idd loci: NRAMP1/SLC11A1 (orthologous to Nramp1/Slc11a1 in Idd5.2), FRAP1 (orthologous to Frap1 in Idd9.2), 4-1BB/CD137/TNFRSF9 (orthologous to 4-1bb/Cd137/Tnrfrsf9 in Idd9.3), CD101/IGSF2 (orthologous to Cd101/Igsf2 in Idd10), B2M (orthologous to B2m in Idd13) and VAV3 (orthologous to Vav3 in Idd18).

Results

Re-sequencing of a total of 110 kb of DNA from 32 or 96 type 1 diabetes cases yielded 220 single nucleotide polymorphisms (SNPs). Sixty-five SNPs, including 54 informative tag SNPs, and a microsatellite were selected and genotyped in up to 1,632 type 1 diabetes families and 1,709 cases and 1,829 controls.

Conclusion

None of the candidate regions showed evidence of association with type 1 diabetes (P values > 0.2), indicating that common variation in these key candidate genes does not play a major role in type 1 diabetes susceptibility in the European ancestry populations studied.

Genetic analysis of SLC11A1 polymorphisms in multiple sclerosis patients

Solute carrier 11a1 (SLC11A1; formerly NRAMP1, where NRAMP stands for natural resistance-associated macrophage protein) is a proton/bivalent cation antiporter that localizes to late endosomes/lysosomes. SLC11A1 regulates macrophage functions that are of potential importance in the induction and/or maintenance of autoimmune diseases such as rheumatoid arthritis, type I diabetes and Crohn's disease. We investigated SLC11A1 gene as a candidate gene for genetic susceptibility to multiple sclerosis (MS) in our population. Four SLC11A1 gene polymorphisms (5'GT repeat, D543N, 1729 + 55del4 and 1729 + 271del4) were analysed in a case-control study of 195 patients with MS and 125 control subjects. We found no evidence of association between SLC11A1 polymorphisms and MS susceptibility in the Spanish population.

Expression of the SLC11A1 (NRAMP1) 5′-(GT)n repeat: Opposite effect in the presence of −237C→T

Association of various autoimmune and infectious diseases with genetic variation in the solute carrier family 11 member 1 (SLC11A1) gene, formerly known as the natural resistance-associated macrophage protein 1 (NRAMP1) gene, is in accordance with its role in iron metabolism and immune function. In this investigation, in vitro studies were performed to determine whether allelic variants in the promoter region of the gene are affected by iron loading, thereby leading to differential expression of SLC11A1. Constructs containing five different SLC11A1 5'-(GT)n polymorphic alleles identified in the South African population (alleles 2, 3, 5, 8, and 9) and a C to T point mutation at nucleotide position -237, both in the absence and presence of allele 3, were cloned into the pGL2-Basic luciferase-reporter vector and transfected into U937 and THP-1 cells. Addition of exogenous stimuli, including interferon-gamma, bacterial lipopolysaccharide, and ferric ammonium citrate, demonstrated significant differences in the ability of these alleles to regulate gene expression. Striking differences were obtained upon iron loading, with allele 3 showing opposite effects in the presence or absence of promoter polymorphism -237C-->T. Our findings provide direct evidence that this promoter polymorphism is functional and support the hypothesis that iron dysregulation mediated by allelic effects of SLC11A1 underlies disease susceptibility linked to infectious and autoimmune conditions.

Genetic factors in the pathogenesis of primary biliary cirrhosis

Current knowledge of the genetic basis of PBC is at best incomplete and at worst poor. Studies so far may be used as a guide to the pitfalls that await unwary investigators and also in deciding where to look and which genes or systems are most likely to yield informative results. The Human Genome Project has revealed a vast array of polymorphism that is too much to contemplate even with the best of current techniques. The crucial processes are the selection of candidates and study design. The strong genetic associations so far in PBC are with chromosomes 6p21.3 and 2q and include; HLA DRBI*08 haplotypes, CTLA4* G and IL1RN-IL1B haplotypes, CASP8, and nramp1. Many of the latter should be considered with caution until confirmed in independent series. Other associations with MBL, APOE and VDR remain to be confirmed. There are also several informative negatives, MMP3 and IL10 for example. It is unlikely that the only genes that influence disease susceptibility and progression in PBC are immunoregulatory genes concerned with T cell immunity. Recent studies indicate a new era for immunogenetics, when genes encoding all immune active proteins may be considered as candidates. One should not concentrate solely on the immune response as recent investigations of mannose binding lectin and apolipoprotein-E testify. One is only just beginning to understand the genetic basis of complex diseases like PBC. The key issues for future investigators are: defining the mechanisms where by self tolerance is broken, defining the mechanisms that determine the rate of disease progression, and identifying genetic markers to predict progression and malignancy. Assessing the genetic basis of variability in disease progression. The significant variation in rate of progression of PBC has led to the hypothesis that genes, in addition to contributing to disease susceptibility, may also determine the rate of disease progression. Several of the studies mentioned earlier have suggested associations between alleles at polymorphic loci and rate of progression . All studies performed to date, however, have been retrospective in nature. One problem inherent in such studies is that of definition of disease progression. One simple definition, that of histological progression to Scheuer stage IV disease , requires liver biopsy. The need to perform repeat biopsies raises ethical problems in cases where there is no other clinical indication. Studies of histologic progression in patients in the control arm of therapeutic trials represent one scenario where repeat biopsy would be indicated. However, the typical time course of such trials is 2 years, insufficient for meaningful assessment of disease progression and natural history, particularly in PBC where there is marked heterogeneity and, as a result, tissue sampling error. Yet, alternative systems for assessing disease progression, such as the Mayo prognostic score, lack sensitivity in any scenario other than existing advanced disease. Outlook for the future. Clinical observations support a significant genetic component to disease susceptibility. Elucidating predisposing genetic associations will markedly assist in understanding the pathophysiology of disease. Investigations to date have been restricted to various community-based case-control association studies, with well-recognized limitations. In future SNP maps and haplotype maps from the Human Genome Project will be available. Studies will require the collection of several well-characterized patients. To meet the required statistical power this will necessitate collaboration on a national and international scale. It is essential that these studies address the relationship between genes and disease progression. The possibility of identifying, in the early stages of disease, patients who are at elevated risk for more rapid progression, would have obvious clinical benefit in terms of patient management and therapy.

Epidemiology of autoimmune liver disease

Primary biliary cirrhosis (PBC), autoimmune hepatitis (AIH) and primary sclerosing cholangitis (PSC) are chronic liver diseases that likely have an autoimmune basis to their pathogenesis. Although significant strides have been made in the clinical management of these conditions, their pathogenesis remains obscure. Understanding of various epidemiological factors may shed light on predisposing or causative factors for these diseases. Most is known about the epidemiology of PBC, with only minimal information on that of PSC and AIH. In this review, the current data on the epidemiology of PBC, AIH and PSC are summarized and suggestions are made for future work in this important area.

Extent and distribution of linkage disequilibrium around the SLC11A1 locus

The SLC11A1 (or NRAMP1) locus on human chromosome 2q35 encodes for the protein solute carrier family 11, member 1. It is expressed in macrophages and involved in the early stages of macrophage priming and activation. Different association studies have shown that the SLC11A1 gene affects susceptibility to infectious diseases and autoimmune inflammatory diseases. Although functional SLC11A1 polymorphisms may account for its role in affecting the susceptibility to these diseases, the positive association can also be because of flanking polymorphisms showing linkage disequilibrium (LD) with this locus. This is the first systematic study to investigate the LD pattern within and around the gene. LD was investigated by genotyping 17 genetic markers in a Chinese population (n=360). The results indicate that LD is maintained at least 110 kb both upstream and downstream of the locus. The complex LD pattern demands that association studies with SLC11A1 should be carried out with both 5' and 3' markers. The strong LD between IL8RB and the 5' SLC11A1 markers also dictates that IL8RB be tested for association with these diseases. Thus, positive association with SLC11A1 should be interpreted cautiously, and IL8RB should also be considered as a potential candidate susceptibility gene unless proven otherwise.

Divalent cation transport and susceptibility to infectious and autoimmune disease: continuation of the Ity/Lsh/Bcg/Nramp1/Slc11a1 gene story

Solute carrier family 11 member a1 (Slc11a1), formerly known as Nramp1/Ity/Lsh/Bcg, is a proton/divalent cation antiporter that regulates susceptibility to infectious and autoimmune disease. Here we review recent studies on (1) the role of Slc11a1 in iron metabolism and iron recycling in macrophages; (2) the use of mouse breeding and introgression of knockouts onto Slc11a1 congenic backgrounds for genes encoding the multiple pleiotropic functions associated with Slc11a1; and (3) associations/linkages of SLC11A1 with human disease and how these relate to functional promoter region polymorphisms.

Inflammatory bowel disease is associated with a novel promoter polymorphism of natural resistance-associated macrophage protein 1 (NRAMP1) gene

Inflammatory bowel diseases (IBD) representing both Crohn's disease and ulcerative colitis are characterized by chronic activation of macrophages. Natural resistance-associated macrophage protein 1 (NRAMP1) gene regulates macrophage activation of antimicrobial activity and has many pleiotropic effects on macrophage functions. To explore the role of the NRAMP1 gene in IBD susceptibility, we examined the promoter sequence of the NRAMP1 gene whose polymorphisms have been reported to influence the transcriptional activity of the NRAMP1 gene. One novel allele (allele 7) and two previously reported alleles (alleles 2 and 3) have been determined in a Japanese population. We investigated the association of IBD with these three alleles. The allele frequency of allele 7 was significantly higher in patients with Crohn's disease (11.1%) and ulcerative colitis (11.2%) than those in the healthy control group (4.5%) (Pc=0.015, Pc=0.018, respectively). Therefore, our findings suggest that the novel promoter polymorphism of the NRAMP1 gene may influence susceptibility to IBD in the Japanese population.

High-level expression of NRAMP1 in peripheral blood cells and tuberculous granulomas from Mycobacterium bovis-infected bovines

By Western blotting, we demonstrate high-level expression of NRAMP1 proteins in peripheral blood cells and granulomas of Mycobacterium bovis-infected bovines. Immunohistochemistry of granulomatous lesions showed heavily labeled epithelioid macrophages and Langhans cells. These data suggest that M. bovis infection enhances NRAMP1 expression and that active tuberculosis can occur despite this response.

Genetic and familial considerations of primary biliary cirrhosis

The genetic basis of human autoimmune diseases is receiving increasing attention. Primary biliary cirrhosis (PBC) is a model autoimmune disease reflective of other organ-specific autoimmune pathology. PBC is an enigmatic autoimmune disease that predominantly affects women and leads to destruction of intrahepatic bile ducts. The serological hallmark of this disease is characterized by antimitochondrial antibodies that specifically react with the E2 components of 2-oxodehydrogenase enzymes, including PDC-E2. There are no clear major histocompatibility complex associations with the development of PBC, despite the observation that first-degree relations of index patients with PBC have a 4-6% prevalence of development of PBC. This risk factor is comparable or higher than any other human autoimmune disease and suggests that a genome-wide approach towards dissection of genetic associations would lead to valuable new insights. In this review, we place these concepts in perspective and highlight in particular the genetic associations in PBC and the importance of studying siblings with PBC who are concordant for disease.

Analysis of the NRAMP1 Gene Implicated in Iron Transport: Association with Multiple Sclerosis and Age Effects

Multiple sclerosis (MS) is believed to be an autoimmune process occurring in genetically susceptible individuals after an appropriate environmental exposure. We have exploited the homogeneous Afrikaner population of European ancestry to investigate the likelihood that iron dysregulation, in association with infectious and/or autoimmune disease susceptibility, may underlie the MS phenotype in a subgroup of patients. The functional Z-DNA forming repeat polymorphism of the natural resistance-associated macrophage protein-1 (NRAMP1) gene was analyzed in 104 patients diagnosed with MS and 522 Caucasian controls. A family-based control group consisting of 32 parental alleles not transmitted to MS offspring was additionally studied to exclude the likelihood of population substructures. Statistically significant differences in allelic distribution were observed between the patient and control samples drawn from the same population (P < 0.01). Evidence is furthermore provided that alleles considered to be detrimental in relation to autoimmune disease susceptibility may be maintained in the population as a consequence of improved survival to reproductive age following infectious disease challenge. Although it remains to be determined whether the disease phenotype in MS patients with allele 5 of the NRAMP1 promoter polymorphism is directly related to dysregulation of iron or modified susceptibility to viral infection and/or autoimmunity, a combination of these processes most likely underlies the disease phenotype in these patients. In view of the emerging role of polymorphic variants in complex diseases and minimizing of possible confounding factors in this association study, we conclude that allelic variation in the NRAMP1 promoter may contribute significantly to MS susceptibility in the South African Caucasian population.