MHC Region Research Articles

Transcriptomic and nuclear architecture of immune cells after LPS activation

Changes in the nuclear positioning of specific genes, depending on their expression status, have been observed in a large diversity of physiological processes. However, gene position is poorly documented for immune cells which have been subjected to activation following bacterial infection. Using a pig model, we focused our study on monocyte-derived macrophages and neutrophils, as they are the first lines of defence against pathogens. We examined whether changes in gene expression due to LPS activation imply that genes have repositioned in the nuclear space. We first performed a transcriptomic analysis to identify the differentially expressed genes and then analysed the networks involved during lypopolysaccharide/interferon gamma activation in monocyte-derived macrophages. This allowed us to select four up-regulated (IL1β, IL8, CXCL10 and TNFα) and four down-regulated (VIM, LGALS3, TUBA3 and IGF2) genes. Their expression statuses were verified by quantitative real-time RT-PCR before studying their behaviour in the nuclear space during macrophage activation by means of 3D fluorescence in situ hybridization. No global correlation was found between gene activity and radial positioning. Only TNFα belonging to the highly transcribed MHC region on chromosome 7 became more peripherally localized in relation to the less decondensed state of its chromosome territory (CT) in activated macrophages. The analysis of gene positioning towards their CT revealed that IL8 increases significantly its tendency to be outside its CT during the activation process. In addition, the gene to CT edge distances increase for the three up-regulated genes (IL8, CXCL10 and TNFα) among the four analysed. Contrarily, the four down-regulated genes did not change their position. The analysis of gene behaviour towards their CT was extended to include neutrophils for three (TNFα, IL8 and IL1β) up- and two (IGF2 and TUBA3) down-regulated genes, and similar results were obtained. The analysis was completed by studying the four up-regulated genes in fibroblasts, not involved in immune response. Our data suggest that relocation in the nuclear space of genes that are differentially expressed in activated immune cells is gene and cell type specific but also closely linked to the entire up-regulation status of their chromosomal regions.

Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

BackgroundSeveral susceptibility genetic variants for autoimmune diseases have been identified. A subset of these polymorphisms displays an opposite risk profile in different autoimmune conditions. This observation open interesting questions on the evolutionary forces shaping the frequency of these alleles in human populations.We aimed at testing the hypothesis whereby balancing selection has shaped the frequency of opposite risk alleles.ResultsSince balancing selection signatures are expected to extend over short genomic portions, we focused our analyses on 11 regions carrying putative functional polymorphisms that may represent the disease variants (and the selection targets). No exceptional nucleotide diversity was observed for ZSCAN23, HLA-DMB, VARS2, PTPN22, BAT3, C6orf47, and IL10; summary statistics were consistent with evolutionary neutrality for these gene regions. Conversely, CDSN/PSORS1C1, TRIM10/TRIM40, BTNL2, and TAP2 showed extremely high nucleotide diversity and most tests rejected neutrality, suggesting the action of balancing selection. For TAP2 and BTNL2 these signatures are not secondary to linkage disequilibrium with HLA class II genes. Nonetheless, with the exception of variants in TRIM40 and CDSN, our data suggest that opposite risk SNPs are not selection targets but rather have accumulated as neutral variants.ConclusionData herein indicate that balancing selection is common within the extended MHC region and involves several non-HLA loci. Yet, the evolutionary history of most SNPs with an opposite effect for autoimmune diseases is consistent with evolutionary neutrality. We suggest that variants with an opposite effect on autoimmune diseases should not be considered a distinct class of disease alleles from the evolutionary perspective and, in a few cases, the opposite effect on distinct diseases may derive from complex haplotype structures in regions with high genetic diversity.

Sequence Capture and Next Generation Resequencing of the MHC Region Highlights Potential Transplantation Determinants in HLA Identical Haematopoietic Stem Cell Transplantation

How cells coordinate the immune system activities is important for potentially life-saving organ or stem cell transplantations. Polymorphic immunoregulatory genes, many of them located in the human major histocompatibility complex, impact the process and assure the proper execution of tolerance-versus-activity mechanisms. In haematopoietic stem cell transplantation, on the basis of fully human leukocyte antigen (HLA)-matched donor–recipient pairs, adverse effects like graft versus leukaemia and graft versus host are observed and difficult to handle. So far, high-resolution HLA typing was performed with Sanger sequencing, but for methodological reasons information on additional immunocompetent major histocompatibility complex loci has not been revealed. Now, we have used microarray sequence capture and targeted enrichment combined with next generation pyrosequencing for 3.5 million base pair human major histocompatibility complex resequencing in a clinical transplant setting and describe 3025 variant single nucleotide polymorphisms, insertions and deletions among recipient and donor in a single sequencing experiment. Taken together, the presented data show that sequence capture and massively parallel pyrosequencing can be used as a new tool for risk assessment in the setting of allogeneic stem cell transplantation.

A study of HLA class I and class II 4-digit allele level in Stevens-Johnson syndrome and toxic epidermal necrolysis

Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are represented by rare but life-threatening cutaneous adverse reactions to different drugs. Previous studies have found that in a Han Chinese population from Taiwan and other Asian Countries, a strong genetic association between HLA-class I alleles (B*15:02, B*58:01) and SJS and TEN was induced by carbamazepine and allopurinol, respectively. To identify genetic markers that covered the MHC region, we carried out a case-control association enrolling 20 Caucasian patients with SJS/TEN. Our patient series included 10 cases related to paracetamol, 7 to allopurinol and 3 to different drugs (plaquenil, itraconazol, nabumetone). Healthy controls were represented by 115 Caucasian bone marrow or stem cell donors. The HLA-A*, B*, C*, DRB1*, DQB1*, DQA1* and DPB1* genotyping were determined. The frequencies of HLA-A*33:03 as well as C*03:02 and C*08:01 were significantly higher in SJS/TEN patient subgroup showing allopurinol drug-induced severe cutaneous adverse reactions (SCAR) as compared to controls (28.6% vs 0%, P=0.00002, Pc=0.0011; 28.6% vs 0%, P=0.00002, Pc=0.001; 28.6% vs 0%, P=0.00002, Pc=0.001, respectively). In the same subgroup the frequencies of B*58:01, DRB1*15:02 and DRB1*13:02 alleles, although considerably higher than in control group (42.8% vs 5.2%, P=0.003; 28.6% vs 1.7%, P=0.005; 28.6% vs 3.5%, P=0.037, respectively), appeared no more statistically different after P correction (Pc=0.248; Pc=0.29; Pc=1.00, respectively). In addition, in 10 of the 20 SJS/TEN patient subgroup with paracetamol-induced SCAR no statistically significant association with HLA alleles could be found. However, in the same SJS/TEN patient subgroup showing allopurinol drug-induced SCAR, haplotype analysis indicated that B*58:01, DRB1*13:02 and DRB1*15:02 alleles, that in a single allele analysis lost statistical significance after P correction, may still confer susceptibility, because the B*58:01-DRB1*13:02 and DRB1*15:02-DQB1*05:02 are positively associated with the disease (14.2% vs 0.43%, P= 0.00001, Pc=0.00028; 14.2% vs 0.43%, P=0.00001, Pc=0.00028, respectively). Our results show that in contrast to SCAR-related to paracetamol, where HLA alleles do not appear to be involved, HLA molecules behave as a strong risk factor for SCAR-related to allopurinol even when a limited number of patients are considered.

A Genome-Wide Association Study Identifies Potential Susceptibility Loci for Hepatotoxicity Due to Various Drugs

Idiosyncratic drug-induced liver injury (DILI) is a leading cause of morbidity and mortality due to medication use yet is poorly studied, in part, due to its low incidence in the general population. Identification of genetic variants associated with these uncommon and difficult to diagnose adverse events could provide clues to underlying mechanisms. Hypothesis: Common genetic variants exist that contribute to DILI susceptibility from multiple drugs. Methods: DNA obtained from 783 individuals of European ancestry who experienced DILI attributed to >200 individual drugs were genotypedwith the Illumina 1Mor 1Mduo beadchip. Source of DNA samples included the following DILI registries: DILIN (401), DILIGEN (242), EUDRAGENE (89), and Malaga (51). Genome Wide Association (GWA) was performed using population controls (n=3001). Potential associations were tested for replication in 190 independent cases from DILIN. Results: GWA revealed a strong association within the MHC region (p 108), which did not replicate in validation cohorts composed of sufficient cases due to the same drug or class. Conclusion: Our replicated association between hepatocellular DILI and STAT4 supports the emerging role of the immune system in DILI susceptibility and suggests that common genetic variation may contribute to DILI susceptibility from multiple drugs. However, the generally negative GWA results suggest that there may be a preponderance of drug-specific genetic risk factors and/or rare genetic variation underlying DILI susceptibility. Therefore, we have begun whole exome and whole genome sequencing of DILI cases caused by the most frequent drugs in our cohorts in search of rarer, high-penetrance drug-specific risk factors.

Novel Susceptibility Loci for Primary Sclerosing Cholangitis Identified by Genome-Wide Association and Replication Analysis

Idiosyncratic drug-induced liver injury (DILI) is a leading cause of morbidity and mortality due to medication use yet is poorly studied, in part, due to its low incidence in the general population. Identification of genetic variants associated with these uncommon and difficult to diagnose adverse events could provide clues to underlying mechanisms. Hypothesis: Common genetic variants exist that contribute to DILI susceptibility from multiple drugs. Methods: DNA obtained from 783 individuals of European ancestry who experienced DILI attributed to >200 individual drugs were genotypedwith the Illumina 1Mor 1Mduo beadchip. Source of DNA samples included the following DILI registries: DILIN (401), DILIGEN (242), EUDRAGENE (89), and Malaga (51). Genome Wide Association (GWA) was performed using population controls (n=3001). Potential associations were tested for replication in 190 independent cases from DILIN. Results: GWA revealed a strong association within the MHC region (p 108), which did not replicate in validation cohorts composed of sufficient cases due to the same drug or class. Conclusion: Our replicated association between hepatocellular DILI and STAT4 supports the emerging role of the immune system in DILI susceptibility and suggests that common genetic variation may contribute to DILI susceptibility from multiple drugs. However, the generally negative GWA results suggest that there may be a preponderance of drug-specific genetic risk factors and/or rare genetic variation underlying DILI susceptibility. Therefore, we have begun whole exome and whole genome sequencing of DILI cases caused by the most frequent drugs in our cohorts in search of rarer, high-penetrance drug-specific risk factors.

HLA DRB1*1503 allelic haplotype predominance and associated immunodysregulation in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a chronic, relapsing, and remitting disease affecting primarily African American females of child bearing age. Familial aggregation of this disease suggests that at least part of the susceptibility for this disease is genetic, although environmental and hormonal influences are also likely to play a role. Early studies of genetic susceptibility to SLE revealed several of the major histocompatibility complex molecules, namely HLA DR, to be linked to SLE. Meta-analysis of genome scans has yielded loci significant for lupus patients, one of which includes the MHC region. Regulatory T cells are immunoregulatory cells that modulate activated immune cells. These cells play a large role in homeostasis of the immune responses and maintenance of immunologic tolerance, i.e., prevention of autoimmunity. Decreased numbers of regulatory T cells have been described in many autoimmune diseases, including systemic lupus erythematosus. Autoantibody production in systemic lupus erythematosus and the resulting immune complex formation and complex deposition into tissues are arguably the central core of immune dysregulation leading to disease manifestations and symptoms. Inability of the immune system to recognize and inhibit autoreactive immune cells in this particular autoimmune disease may be the result of inappropriate numbers and function of regulatory T cells. This study aims to characterize the immune cell population in patients from our community suffering from systemic lupus erythematosus and to prove that these patients exhibit a unique cellular profile compared to healthy age, race and gender matched control subjects. Surprisingly, our findings demonstrate that patients from the local Mississippi area exhibit increased proportions of CD25 + FoxP3 + regulatory T cells and CD25 + FoxP3 − T cells (of CD45 + CD3 + CD4 + helper T cells) as compared to healthy controls. HLA tissue-typing of these lupus patients revealed a prominent subgroup (~ 30%) of patients possessing the HLA DRB1*1503 allele. The investigation of this subgroup demonstrated regulatory T cell composition similar to that of the total lupus group and to that of the non-HLA DRB1*1503 subgroup. Genetic analysis for molecular gene expression levels of various lupus-associated genes by real-time PCR demonstrated a unique profile as compared to healthy controls. Increased gene expression of FoxP3 together with decreased gene expression levels of GATA3, TNFAIP3, and TNFSF4 suggest that variations in gene products compared to healthy controls may be playing a role in the immune cell dysregulation and disproportionate CD25 + FoxP3 + regulatory T cells.

P.4.016 Follow-up of schizophrenia genome-wide association studies implicates the MHC region in cognition

Cognitive dysfunction is a core feature of schizophrenia. Growing evidence indicates that a wide variety of genetic mutations and polymorphisms impact cognition and may thus be implicated in various aspects of this mental disorder. Despite differences between human and rodent brain structure and function, genetic mouse models have contributed critical information about brain mechanisms involved in cognitive processes. Here, we summarize discoveries of genetic modifications in mice that impact cognition. Based on functional hypotheses, gene modifications within five model systems are described: 1) dopamine (D1, D2, D3, D4, D5, DAT, COMT, MAO); 2) glutamate (GluR-A, NR1, NR2A, NR2B, GRM2, GRM3, GLAST); 3) GABA (α5, γ2, α4, δGABAA, GABAB(1), GAT1); 4) acetylcholine (nAChRβ2, α7, CHRM1); and 5) calcium (CaMKII-α, neurogranin, CaMKKβ, CaMKIV). We also consider other risk-associated genes for schizophrenia such as dysbindin (DTNBP1), neuregulin (NRG1), disrupted-in-schizophrenia1 (DISC1), reelin and proline dehydrogenase (PRODH). Because of the presumed importance of environmental factors, we further consider genetic modifications within the stress-sensitive systems of corticotropin-releasing factor (CRF), brain-derived neurotrophic factor (BDNF) and the endocannabinoid systems. We highlight the missing information and limitations of cognitive assays in genetically modified mice models relevant to schizophrenia pathology.This article is part of a Special Issue entitled ‘Schizophrenia’

A Bayesian Method for Disentangling Dependent Structure of Epistatic Interaction

Problem statement: We propose a Bayesian method (RBP) to recursively infer the independence structure of epistatic interactions in case-control study. Approach: Based on the results of BEAM2, RBP can powerfully detect the marginal and conditional independence within interacting SNPs even in the complicated interaction cases. Results: We did extensive simulations to test RBP and compare it with stepwise logistic regression. Simulation results show that this approach is more powerful than stepwise logistic regression in detecting in marginal independence and conditional independence as well as more complicated dependence structure. We then applied BEAM2 and RBP on dbMHC Type 1 Diabetes (T1D) data and we found in MHC region, genes DRB1 and DQB1 are associated with T1D with saturated interaction structure which is consistent with the current knowledge of haplotype effect of these two genes on T1D. Conclusion: RBP is a powerful method to infer detailed dependence structures in epistatic interactions.

Drug Induced Hypersensitivity and the HLA Complex

Drug-induced hypersensitivity reactions are of major concern and present a burden for national healthcare systems due to their often severe nature, high rate of hospital admissions and high mortality. They manifest with a wide range of symptoms and signs, and can be initiated by a wide range of structurally diverse chemical compounds. The pathophysiological mechanisms underlying hypersensitivity reactions are not well understood, but it is thought that they are immune mediated. MHC region on Chromosome 6 contains many genes with immune function. Classical MHC molecules are highly polymorphic cell surface glycoproteins whose function is to present peptide antigens to T cells. In addition to conferring protection from some diseases, HLA alleles are also associated with an increased risk of other diseases, including drug-induced hypersensitivity. Pharmacogenetic approach to predict the risk of drug-induced hypersensitivity has been established for several drugs. We will discuss the progress of hypersensitivity pharmacogenetics over the last few years and focus on current efforts of the international community to develop consortia which aim to standardize disease phenotypes and to identify affected individuals through international collaborations. In addition, we will discuss the clinical utility of HLA typing as predictive or diagnostic testing for drug-induced hypersensitivity.

Variants in MHC, LCE and IL12B have epistatic effects on psoriasis risk in Chinese population

Psoriasis has long been considered as a complex disease, and gene-gene or gene-environment interactions may jointly influence the etiology for psoriasis. We evaluated the associations of single nucleotide polymorphisms (SNPs) in MHC region, and determined the epistasis and combined effects of MHC locus and IL12B, LCE on risk for psoriasis. We genotyped SNP rs1265181 (MHC) in 5067 cases and 6404 controls, combining with the prior GWAS data (1139 cases and 1132 controls), we explored the genetic interaction among MHC locus, LCE and IL12B by using logistic regression analysis. We evaluated the combined effects of MHC locus and two non-MHC loci in the combined sample of 6206 cases and 7536 controls. Extremely high significance of association was detected between rs1265181 and psoriasis (p combined < 10E--300, OR = 16.52, 95% CI: 15.28-18.44). We observed significant interactions between MHC and LCE (p = 0.0016) and between MHC and IL12B (p = 0.0036). The risk increased some 26-fold in individuals with risk alleles in both MHC and LCE as compared with those without risk alleles, and individual carrying risk alleles of MHC and IL12B has around 36-fold higher risk of psoriasis than those with protective alleles. This study provides evidence for the epistatic effects between MHC locus and LCE, IL12B genes. Besides, we suggest that MHC might be the main effect gene on the risk for psoriasis. This data may contribute to our understanding of psoriasis genetic interactions and account for the additional risk of certain patients to develop psoriasis.

Structure of a Classical MHC Class I Molecule That Binds “Non-Classical” Ligands

Author SummaryProteins encoded by the major histocompatibility complex (MHC) play crucial roles in vertebrate immune systems, presenting pathogen-derived protein fragments to receptors on effector cells. In contrast, some non-classical MHC class I proteins such as CD1 molecules possess a hydrophobic groove that allows them to display lipids. Chicken MHC-Y is a genetic region outside the core MHC that harbors several immune-related genes, among them YF1*7.1, which encodes a protein whose structure we solved in this study. YF1*7.1 is an MHC class I molecule that exhibits the architecture typical of classical MHC class I antigens but possesses a hydrophobic binding groove that binds non-peptidic ligands. By using lipid-binding assays, we show that this molecule can indeed bind lipids. Therefore, YF1*7.1 bridges, at least in structural terms, the traditional gap between classical and non-classical MHC class I molecules. Lipid-binding YF1 proteins might serve the chicken to enlarge its otherwise very small repertoire of antigen-presenting MHC class I molecules. Furthermore, comparative analyses of the two protein subunits of classical MHC molecules revealed a structural feature in chickens that appears to be shared by non-mammalian but not by mammalian vertebrates. This unique feature is indicative of a structure-dependent co-evolution of two genetically unlinked genes in non-mammalian species.

A three-way interplay of DR4, autoantibodies and synovitis in biopsy-proven idiopathic inflammatory myositis

The aim of this study was to determine the HLA and autoantibody associations of patients with histologically confirmed idiopathic inflammatory myositis (IIM). Serum and DNA were archived from South Australian patients with biopsy-proven dermatomyositis (DM), polymyositis (PM) and inclusion body myositis (IBM). HLA typing for Class I and II alleles was performed by serology and DNA-based technology, respectively, for 133 myositis patients and 166 Caucasian population-based controls. Myositis-specific and myositis-associated autoantibodies were detected by line immunoblot. All alleles of the 8.1AH were associated with myositis susceptibility. The B8-DR3 haplotype fragment conferred the strongest susceptibility (OR 2.9, 95% CI 1.8-4.6), and the B-DR region of other ancestral haplotypes was associated with myositis subgroups. Autoantibodies were present in 42/130 (32%) IIM patients and were more frequent in DM (11/17, 65%) than PM (23/70, 33%) or IBM (8/43, 19%), P = 0.002. Autoantibodies were associated with DRB1 03 (P = 0.0005) but also with DRB1 04 (P = 0.004). The frequency of autoantibodies in the three myositis subgroups mirrored the frequency of DR4. Polyarthralgia (±synovitis) was more common in DM/PM (30/76, 39%) than IBM (3/32, 9%), P = 0.004, and there was a strong ordinal association between the prevalence of autoantibodies and polyarthralgia ± synovitis (proportional OR = 5.5, 95% CI 2.3-13.7, P = 0.0004). The central MHC region confers the strongest susceptibility for IIM and also modulates disease phenotype. Our findings reveal a novel association of autoantibodies with DR4 and with arthralgia/synovitis in IIM and raise the possibility of a genetically (DR4) determined citrullination of myositis autoantigens expressed in muscle and synovium.

Genetic susceptibility to Behcet's disease: role of genes belonging to the MHC region

To review the progress in the field of MHC-related genetic susceptibility to Behçet's disease (BD). Systematic review of the English literature between 1 January 1980 and 31 January 2010 using Medline. Case-control, population-based, observational cohort studies investigating the association between BD and HLA-B*51 subtypes, classical and non-classical HLA alleles and other HLA-related genes were selected. The geographical distribution of BD and these susceptibility genes was also taken into consideration. Case and familial case reports were excluded except for case series with more than two patients. Ninety articles plus 17 obtained from other sources were included in the systematic review. We have found high evidence that a core component of genetic susceptibility to BD is within the MHC region being primarily related to an HLA-B*51 subtype: HLA-B*5101/B*510101. Moreover, HLA-A*26, HLA-B*15, HLA-B*5701 and TNF-α -1031C were independently associated with BD. Data suggest that other HLA (HLA-C, HLA-DR) and HLA-related [MHC Class I chain-related gene A (MIC-A), TNF-α] genes may play a role in BD co-susceptibility or pathogenesis. Finally, the distinctive geographical distribution of BD suggested an evolutionary selection of HLA-B*51 subtypes as the major susceptibility factors for BD. Further studies must be addressed to clarify the functional relevance of the different genes found to be associated with disease susceptibility and the potential interactions between genes located within and outside the MHC region.

Most genome-wide significant susceptibility loci for schizophrenia and bipolar disorder reported to date cross-traditional diagnostic boundaries

Recent findings from genetic epidemiology and from genome-wide association studies point strongly to a partial overlap in the genes that contribute susceptibility to schizophrenia and bipolar disorder (BD). Previous data have also directly implicated one of the best supported schizophrenia-associated loci, zinc finger binding protein 804A (ZNF804A), as showing trans-disorder effects, and the same is true for one of the best supported bipolar loci, calcium channel, voltage-dependent, L type, alpha 1C subunit (CACNA1C) which has also been associated with schizophrenia. We have undertaken a cross-phenotype study based upon the remaining variants that show genome-wide evidence for association in large schizophrenia and BD meta-analyses. These comprise in schizophrenia, SNPs in or in the vicinity of transcription factor 4 (TCF4), neurogranin (NRGN) and an extended region covering the MHC locus on chromosome 6. For BD, the strongly supported variants are in the vicinity of ankyrin 3, node of Ranvier (ANK3) and polybromo-1 (PBRM1). Using data sets entirely independent of their original discoveries, we observed strong evidence that the PBRM1 locus is also associated with schizophrenia (P = 0.00015) and nominally significant evidence (P < 0.05) that the NRGN and the extended MHC region are associated with BD. Moreover, considering this highly restricted set of loci as a group, the evidence for trans-disorder effects is compelling (P = 4.7 × 10(-5)). Including earlier reported data for trans-disorder effects for ZNF804A and CACNA1C, six out of eight of the most robustly associated loci for either disorder show trans-disorder effects.

PATU11 IL2RA and CD226 genotypes influence multiple sclerosis disease outcome

IntroductionMS is a chronic inflammatory disorder of the central nervous system. Whole genome analysis has identified discrete chromosomal regions outside the most powerfully associated MHC region that might harbour susceptibility...

45-OR: Fine-Mapping of MHC Region Variants in Juvenile Idiopathic Arthritis (JIA) Reveals Evidence of Additional Predisposing Sites Telomeric to Class I

45-OR: Fine-Mapping of MHC Region Variants in Juvenile Idiopathic Arthritis (JIA) Reveals Evidence of Additional Predisposing Sites Telomeric to Class I

Genes Within the MHC Region Have a Dramatic Influence on Radiation-Enhanced Atherosclerosis in Mice

C3H/HeJ (C3H) mice develop much smaller atherosclerotic lesions than C57BL/6 (B6) mice when deficient in apolipoprotein E (apoE⁻(/)⁻) or fed an atherogenic diet. The 2 strains differ in H2 haplotypes, with B6 having H2(b) and C3H having H2(k). C3.SW-H2(b)/SnJ (C3.SW) is a congenic strain of C3H/HeJ in which H2(k) is replaced with H2(b). We performed bone marrow transplantation and found that atherosclerosis-resistant C3.SW.apoE⁻(/)⁻ mice reconstituted with bone marrow from either C3.SW.apoE⁻(/)⁻ or B6.apoE⁻(/)⁻ mice after lethal irradiation had significantly larger atherosclerotic lesions than B6.apoE⁻(/)⁻ mice receiving identical treatments and much larger lesions than C3H.apoE⁻(/)⁻ mice reconstituted with syngeneic bone marrow. For syngeneic transplantation, C3.SW.apoE⁻(/)⁻ mice exhibited a 21-fold increase in lesion size over C3H.apoE⁻(/)⁻ mice (152 800±21 937 versus 7060±2290 μm²/section) and a near 4-fold increase over B6.apoE⁻(/)⁻ mice (40 529±4675 μm²/section). C3.SW.apoE⁻(/)⁻ mice reconstituted with syngeneic marrow exhibited enhanced lesion formation relative to those reconstituted with B6 marrow (152 800±21 937 versus 107 000±9374 μm²/section; P=0.067). Sublethal irradiation led to a 6-fold increase of lesion size in C3.SW.apoE⁻(/)⁻ mice (9795±2804 versus 1550±607 μm²/section; P=0.008). Wild-type C3.SW mice reconstituted with apoE(+/+) or apoE⁻(/)⁻ bone marrow had significantly larger atherosclerotic lesions than C3H mice receiving identical treatments on an atherogenic diet. These results indicate that gene(s) within the H2 region have a dramatic impact on radiation-enhanced atherosclerosis, and their effect is conveyed partially through bone marrow-derived cells.

Genome-wide mapping of Quantitative Trait Loci for fatness, fat cell characteristics and fat metabolism in three porcine F2 crosses

BackgroundQTL affecting fat deposition related performance traits have been considered in several studies and mapped on numerous porcine chromosomes. However, activity of specific enzymes, protein content and cell structure in fat tissue probably depend on a smaller number of genes than traits related to fat content in carcass. Thus, in this work traits related to metabolic and cytological features of back fat tissue and fat related performance traits were investigated in a genome-wide QTL analysis. QTL similarities and differences were examined between three F2 crosses, and between male and female animals.MethodsA total of 966 F2 animals originating from crosses between Meishan (M), Pietrain (P) and European wild boar (W) were analysed for traits related to fat performance (11), enzymatic activity (9) and number and volume of fat cells (20). Per cross, 216 (M × P), 169 (W × P) and 195 (W × M) genome-wide distributed marker loci were genotyped. QTL mapping was performed separately for each cross in steps of 1 cM and steps were reduced when the distance between loci was shorter. The additive and dominant components of QTL positions were detected stepwise by using a multiple position model.ResultsA total of 147 genome-wide significant QTL (76 at P < 0.05 and 71 at P < 0.01) were detected for the three crosses. Most of the QTL were identified on SSC1 (between 76-78 and 87-90 cM), SSC7 (predominantly in the MHC region) and SSCX (in the vicinity of the gene CAPN6). Additional genome-wide significant QTL were found on SSC8, 12, 13, 14, 16, and 18. In many cases, the QTL are mainly additive and differ between F2 crosses. Many of the QTL profiles possess multiple peaks especially in regions with a high marker density. Sex specific analyses, performed for example on SSC6, SSC7 and SSCX, show that for some traits the positions differ between male and female animals. For the selected traits, the additive and dominant components that were analysed for QTL positions on different chromosomes, explain in combination up to 23% of the total trait variance.ConclusionsOur results reveal specific and partly new QTL positions across genetically diverse pig crosses. For some of the traits associated with specific enzymes, protein content and cell structure in fat tissue, it is the first time that they are included in a QTL analysis. They provide large-scale information to analyse causative genes and useful data for the pig industry.

Reply to Dlouha et al

We appreciate the opportunity to reply to the letter by Dlouha et al,1 who have attempted to replicate the association of the FTO variant rs17818902 with obesity that we have recently identified in a self-contained population of Sorbs from Germany.2 To test the SNP in a population closely related to the Sorbs, the authors genotyped this polymorphism in a Czech–Slavonic population. They failed to replicate the initial association and postulated that gene–gene and/or gene–environmental interactions might explain variability in the exact role of this variant in the pathogenesis of obesity in different populations. We agree that a different definition of the investigated phenotype (BMI) is unlikely to explain the observed discrepancy between Czechs and Sorbs. Even though no major differences in genetic background between two neighbouring middle-European Slavonic populations can be assumed,3 recent studies provide strong evidence that population structure represents a well-recognized challenge for disease-association studies, and that spurious associations can arise if genetic structure is not adequately accounted for.4 So far, there is no straightforward explanation for different effect sizes, or even effect directions, of recently identified susceptibility loci in diverse populations (also if ethnic background is comparable). Even if the combined effect in a meta-analysis strongly supports a genetic association the variant does not show replicable effects in all investigated samples. This cannot be explained exclusively by sample size, allele frequencies or phenotypic distribution. As geographic origin of a sample has to be considered when evaluating genome-wide association studies among Europeans,4 the same may be true when attempting to replicate initial association findings. Using principal component analysis we are currently evaluating the genetic variation between Slavonic populations (Sorbs, Czechs, and Poles) and Germans. Our preliminary data indicate that the Sorbs were most closely related to the Poles, but measures such as Fst are summaries and do not necessarily capture all kinds of changes in a certain genetic region. When we investigated the proportion of individuals with at least one other individual IBS at all SNPs across random genomic regions (methods based on Kong et al5), we found that IBS sharing in the Sorbs was much greater compared with that in outbred populations, such as the controls from the WTCCC.6 The proportions of subjects who have at least one other individual with IBS⩾1 at all SNPs across the chromosome 15-long and MHC region were 29.3 and 40.7%, respectively, in the Sorbs compared with 0.8 and 10.2%, respectively, in the WTCCC sample set. We would not necessarily expect to see association at exactly the same SNP because of possible allelic heterogeneity. Moreover, linkage disequilibrium patterns are also likely to be different and, although we cannot provide a definitive explanation for the discrepancies observed, we believe that a unique population history of the Sorbs may contribute to these different associations. Despite failing to replicate the findings of the Sorbian study in the present paper by Dlouha et al,1 it is noteworthy that the relevance of the third intron of FTO is supported by analyses of patterns of selection in the FTO region. These analyses show signatures of recent selection at the FTO locus in human populations,7 and the strongest signal is observed in the third intron, the region in which the strong association with BMI in the Sorbs was recently described.2 Resequencing studies will be required to further elucidate the functional variants behind the association signals. Furthermore, the possible impact of factors such as epigenetics and the effects of rare variants not covered by the available assays should be considered. Last, but not the least, we are aware of the possibility that the finding in Sorbs may be false positive. Given that the finite size of the Sorbian population limited further internal replication, we encourage and appreciate replication attempts by independent groups such as the one reported by Dlouha et al.1