Genome-wide association analysis reveals the associations of NPHP4, TYW1-AUTS2 and SEMA6D for Behçet's disease and HLA-B*46:01 for its intestinal involvement

BACKGROUND

Intestinal involvement in Behçet's disease (BD) is associated with poor prognosis and is more prevalent in East Asian than in Mediterranean populations. Identifying the genetic causes of intestinal BD is important for understanding the pathogenesis and for appropriate treatment of BD patients.

METHODS

We performed genome-wide association studies (GWAS) and imputation/replication genotyping of human leukocyte antigen (HLA) alleles for 1,689 Korean and Turkish patients with BD (including 379 patients with intestinal BD) and 2,327 healthy controls, followed by replication using 593 Japanese patients with BD (101 patients with intestinal BD) and 737 healthy controls. Stratified cross-phenotype analyses were performed for 1) overall BD, 2) intestinal BD, and 3) intestinal BD without association of overall BD.

RESULTS

We identified three novel genome-wide significant susceptibility loci including NPHP4 (rs74566205; P=1.36 × 10-8), TYW1-AUTS2 (rs60021986; P=1.14 × 10-9), and SEMA6D (rs4143322; P=5.54 × 10-9) for overall BD, and a new association with HLA-B*46:01 for intestinal BD (P=1.67 × 10-8) but not for BD without intestinal involvement. HLA peptide binding analysis revealed that Mycobacterial peptides, have a stronger binding affinity to HLA-B*46:01 compared to the known risk allele HLA-B*51:01.

CONCLUSIONS

HLA-B*46:01 is associated with the development of intestinal BD; NPHP4, TYW1-AUTS2, and SEMA6D are susceptibility loci for overall BD.

Genome-wide association study of health and production traits in meat sheep

Genotypes are currently widely used in animal breeding programmes to enhance the speed of genetic progress. With sufficient data, a Genome-Wide Association Study (GWAS) can be performed to identify informative markers. The aim of this study was to investigate the genetic background of health (footrot and mastitis) and production (birth weight, weaning weight, scan weight, and fat and muscle depth) traits using the available phenotypic and Single Nucleotide Polymorphism (SNP) data collected on the UK Texel sheep population. Initially, 10 193 genotypes were subject to quality control, leaving 9 505 genotypes for further analysis. Selected genotypes, recorded on four different Illumina chip types from low density (15 k SNPs) to high density (606 006 SNPs), were imputed to a subset of 45 686 markers from 50 k array, distributed on 27 chromosomes. Phenotypes collected on 32 farms across the UK for footrot and mastitis and extracted from the UK National database (iTexel) for the production traits were used along with pre-estimated variance components to obtain de-regressed breeding values and used to perform GWAS. Results showed three SNPs being significant on the genome-wise level ('OAR8_62240378.1' on chromosome 8 for birth weight, 's14444.1' on chromosome 19 for weaning weight and 's65197.1' on chromosome 23 for scan weight). Fourteen subsequent SNPs were found to be significant at the chromosome-wise level. These SNPs are located within or close to previously reported QTLs impacting on animal health (such as faecal egg count or somatic cell count) and production (such as body or carcass weight and fat amount). These results indicate that the studied traits are highly polygenic with complex genetic architecture.

The interleukin-11 receptor variant p.W307R results in craniosynostosis in humans

Craniosynostosis is characterized by the premature fusion and ossification of one or more of the sutures of the calvaria, often resulting in abnormal features of the face and the skull. In cases in which growth of the brain supersedes available space within the skull, developmental delay or cognitive impairment can occur. A complex interplay of different cell types and multiple signaling pathways are required for correct craniofacial development. In this study, we report on two siblings with craniosynostosis and a homozygous missense pathogenic variant within the IL11RA gene (c.919 T > C; p.W307R). The patients present with craniosynostosis, exophthalmos, delayed tooth eruption, mild platybasia, and a basilar invagination. The p.W307R variant is located within the arginine-tryptophan-zipper within the D3 domain of the IL-11R, a structural element known to be important for the stability of the cytokine receptor. Expression of IL-11R-W307R in cells shows impaired maturation of the IL-11R, no transport to the cell surface and intracellular retention. Accordingly, cells stably expressing IL-11R-W307R do not respond when stimulated with IL-11, arguing for a loss-of-function mutation. In summary, the IL-11R-W307R variant, reported here for the first time to our knowledge, is most likely the causative variant underlying craniosynostosis in these patients.

Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants

The discovery of genetic loci associated with complex diseases has outpaced the elucidation of mechanisms of disease pathogenesis. Here we conducted a genome-wide association study (GWAS) for coronary artery disease (CAD) comprising 181,522 cases among 1,165,690 participants of predominantly European ancestry. We detected 241 associations, including 30 new loci. Cross-ancestry meta-analysis with a Japanese GWAS yielded 38 additional new loci. We prioritized likely causal variants using functionally informed fine-mapping, yielding 42 associations with less than five variants in the 95% credible set. Similarity-based clustering suggested roles for early developmental processes, cell cycle signaling and vascular cell migration and proliferation in the pathogenesis of CAD. We prioritized 220 candidate causal genes, combining eight complementary approaches, including 123 supported by three or more approaches. Using CRISPR-Cas9, we experimentally validated the effect of an enhancer in MYO9B, which appears to mediate CAD risk by regulating vascular cell motility. Our analysis identifies and systematically characterizes >250 risk loci for CAD to inform experimental interrogation of putative causal mechanisms for CAD.

Animal Board Invited Review: Meta-analysis of genetic parameters for resilience and efficiency traits in goats and sheep

Genetic selection focused purely on production traits has proven very successful in improving the productive performance of livestock. However, heightened environmental and infectious disease challenges have raised the need to also improve the resilience of animals to such external stressors, as well as their efficiency in utilising available resources. A better understanding of the relationship between efficiency and production and health traits is needed to properly account for it in breeding programmes and to produce animals that can maintain high production performance in a range of environmental conditions with minimal environmental footprint. The aim of this study was to perform a meta-analysis of genetic parameters for production, efficiency and health traits in sheep and goats. The dataset comprised 963 estimates of heritability and 572 genetic correlations collated from 162 published studies. A threelevel meta-analysis model was fitted. Pooled heritability estimates for milk production traits ranged between 0.27 ± 0.03 and 0.48 ± 0.13 in dairy goats and between 0.21 ± 0.06 and 0.33 ± 0.07 in dairy sheep. In meat sheep, the heritability of efficiency traits ranged from 0.09 ± 0.02 (prolificacy) up to 0.32 ± 0.14 (residual feed intake). For health traits, pooled heritability was 0.07 ± 0.01 (faecal egg count) and 0.21 ± 0.01 (somatic cell score) in dairy goats and 0.14 ± 0.04 (faecal egg count) and 0.13 ± 0.02 (somatic cell score) in dairy sheep. In meat sheep, the heritability of disease resistance and survival traits ranged between 0.07 ± 0.02 (mastitis) and 0.50 ± 0.10 (breech strike). Pooled estimates of genetic correlations between resilience and efficiency traits in dairy goats were not significantly different from zero with the exception of somatic cell score and fat content (-0.19 ± 0.01). In dairy sheep, only the unfavourable genetic correlation between somatic cell score and protein content (0.12 ± 0.03) was statistically significant. In meat sheep only, the correlations between growth and faecal egg count (-0.28 ± 0.11) as well as between growth and dagginess (-0.33 ± 0.13) were statistically significant and favourable. Results of this meta-analysis provide evidence of genetic antagonism between production and health in dairy sheep and goats. This was not observed in meat sheep where most of the pooled estimates had high standard errors and were non-significant. Based on the obtained results, it seems feasible to simultaneously improve efficiency and health in addition to production by including the different types of traits in the breeding goal. However, a better understanding of potential trade-offs between these traits would be beneficial. Particularly, more studies focused on reproduction and resilience traits linked to the animal's multi-trait response to challenges are required.

Discovery of hidden pedigree errors combining genomic information with the genomic relationship matrix in Texel sheep

Genomic variants such as Single Nucleotide Polymorphisms and animal pedigree are now used widely in routine genetic evaluations of livestock in many countries. The use of genomic information not only can be used to enhance the accuracy of prediction but also to verify pedigrees for animals that are extensively managed using natural mating and enabling multiple-sire mating groups to be used. By so doing, the rate of genetic gain is enhanced, and any bias associated with incorrect pedigrees is removed. This study used a set of 8 764 sheep genotypes to verify the pedigree based on both the conventional opposing homozygote method as well as a novel method when combined with the inclusion of the genomic relationship matrix (GRM). The genomic relationship coefficients between verified pairs of animals showed on average a relationship of 0.50 with parent, 0.25 with grandparent, 0.13 with great grandparent, 0.50 with full-sibling and 0.27 with half-sibling. Minimum obtained values from these verified pairs were then used as thresholds to determine the pedigree for unverified pairs of animals, to detect potential errors in the pedigree. Using a case study from a population partially genotyped UK sheep, the results from this study illustrate a powerful way to resolve parentage inconsistencies, when combining the conventional 'opposing homozygote' method using genomic information together with GRM for pedigree checking. In this way, previously undetected pedigree errors can be resolved.

Shared Genetics of Multiple System Atrophy and Inflammatory Bowel Disease

Background:

Multiple system atrophy (MSA) is a rare neurodegenerative disease characterized by intracellular accumulations of α-synuclein and nerve cell loss in striatonigral and olivopontocerebellar structures. Epidemiological and clinical studies have reported potential involvement of autoimmune mechanisms in MSA pathogenesis. However, genetic etiology of this interaction remains unknown. We aimed to investigate genetic overlap between MSA and 7 autoimmune diseases and to identify shared genetic loci.

Methods:

Genome-wide association study summary statistics of MSA and 7 autoimmune diseases were combined in cross-trait conjunctional false discovery rate analysis to explore overlapping genetic background. Expression of selected candidate genes was compared in transgenic MSA mice and wild-type mice. Genetic variability of candidate genes was further investigated using independent whole-exome genotyping data from large cohorts of MSA and autoimmune disease patients and healthy controls.

Results:

We observed substantial polygenic overlap between MSA and inflammatory bowel disease and identified 3 shared genetic loci with leading variants upstream of the DENND1B and RSP04 genes, and in intron of the C7 gene. Further, the C7 gene showed significantly dysregulated expression in the degenerating midbrain of transgenic MSA mice compared with wild-type mice and had elevated burden of protein-coding variants in independent MSA and inflammatory bowel disease cohorts.

Conclusion:

Our study provides evidence of shared genetic etiology between MSA and inflammatory bowel disease with an important role of the C7 gene in both phenotypes, with the implication of immune and gut dysfunction in MSA pathophysiology.

The Macrophage Migration Inhibitory Factor (MIF) Promoter Polymorphisms (rs3063368, rs755622) Predict Acute Kidney Injury and Death after Cardiac Surgery

Background: Macrophage Migration Inhibitory Factor (MIF) is highly elevated after cardiac surgery and impacts the postoperative inflammation. The aim of this study was to analyze whether the polymorphisms CATT_5–7 (rs5844572/rs3063368,“-794”) and G>C single-nucleotide polymorphism (rs755622,-173) in the MIF gene promoter are related to postoperative outcome. Methods: In 1116 patients undergoing cardiac surgery, the MIF gene polymorphisms were analyzed and serum MIF was measured by ELISA in 100 patients. Results: Patients with at least one extended repeat allele (CATT₇) had a significantly higher risk of acute kidney injury (AKI) compared to others (23% vs. 13%; OR 2.01 (1.40–2.88), p = 0.0001). Carriers of CATT₇ were also at higher risk of death (1.8% vs. 0.4%; OR 5.12 (0.99–33.14), p = 0.026). The GC genotype was associated with AKI (20% vs. GG/CC:13%, OR 1.71 (1.20–2.43), p = 0.003). Multivariate analyses identified CATT₇ predictive for AKI (OR 2.13 (1.46–3.09), p < 0.001) and death (OR 5.58 (1.29–24.04), p = 0.021). CATT₇ was associated with higher serum MIF before surgery (79.2 vs. 50.4 ng/mL, p = 0.008). Conclusion: The CATT₇ allele associates with a higher risk of AKI and death after cardiac surgery, which might be related to chronically elevated serum MIF. Polymorphisms in the MIF gene may constitute a predisposition for postoperative complications and the assessment may improve risk stratification and therapeutic guidance.

Protein-coding variants contribute to the risk of atopic dermatitis and skin-specific gene expression

BACKGROUND

Fifteen percent of atopic dermatitis (AD) liability-scale heritability could be attributed to 31 susceptibility loci identified by using genome-wide association studies, with only 3 of them (IL13, IL-6 receptor [IL6R], and filaggrin [FLG]) resolved to protein-coding variants.

OBJECTIVE

We examined whether a significant portion of unexplained AD heritability is further explained by low-frequency and rare variants in the gene-coding sequence.

METHODS

We evaluated common, low-frequency, and rare protein-coding variants using exome chip and replication genotype data of 15,574 patients and 377,839 control subjects combined with whole-transcriptome data on lesional, nonlesional, and healthy skin samples of 27 patients and 38 control subjects.

RESULTS

An additional 12.56% (SE, 0.74%) of AD heritability is explained by rare protein-coding variation. We identified docking protein 2 (DOK2) and CD200 receptor 1 (CD200R1) as novel genome-wide significant susceptibility genes. Rare coding variants associated with AD are further enriched in 5 genes (IL-4 receptor [IL4R], IL13, Janus kinase 1 [JAK1], JAK2, and tyrosine kinase 2 [TYK2]) of the IL13 pathway, all of which are targets for novel systemic AD therapeutics. Multiomics-based network and RNA sequencing analysis revealed DOK2 as a central hub interacting with, among others, CD200R1, IL6R, and signal transducer and activator of transcription 3 (STAT3). Multitissue gene expression profile analysis for 53 tissue types from the Genotype-Tissue Expression project showed that disease-associated protein-coding variants exert their greatest effect in skin tissues.

CONCLUSION

Our discoveries highlight a major role of rare coding variants in AD acting independently of common variants. Further extensive functional studies are required to detect all potential causal variants and to specify the contribution of the novel susceptibility genes DOK2 and CD200R1 to overall disease susceptibility.

ZNF133 is associated with infliximab responsiveness in patients with inflammatory bowel diseases

BACKGROUND AND AIM

Infliximab has been widely prescribed for treating inflammatory bowel disease (IBD). However, the response rates to infliximab differ among patients. Therefore, we aimed to identify the genetic and clinical markers that predict infliximab response.

METHODS

A total of 139 Korean patients with IBD who received infliximab were classified according to infliximab response as follows: (i) primary response vs nonresponse and (ii) sustained response vs loss of response. We performed an association study using whole-exome sequencing data to identify genetic variants associated with infliximab response. Candidate variants were validated in 77 German patients with IBD. Stepwise multivariate logistic regression was performed to identify predictors.

RESULTS

We found five candidate variants that were associated with primary nonresponse to infliximab (P < 5 × 10^-6 ). Of the five variants, rs2228273 in ZNF133 was validated in German (combined P = 6.49 × 10^-7 ). We also identified the best genetic variant (rs9144, P = 4.60 × 10^-6 ) associated with the loss of infliximab response. In multivariate regression analysis, rs2228273 (P = 2.10 × 10^-5 ), concurrent azathioprine/6-mercaptopurine use, and bodyweight at the first infliximab use (< 50 kg) were associated with primary nonresponse. In addition, the Crohn's disease activity index at the first infliximab use and rs9144 (P = 0.001) were independently associated with the loss of response in patients with Crohn's disease.

CONCLUSIONS

We identified clinical and genetic markers associated with infliximab response in IBD patients. Our findings could provide insights to maximize the efficacy of infliximab therapy in IBD patients.

Genetic markers associated with long-term cardiovascular outcome in kidney transplant recipients

There is a clear genetic contribution to the risk of cardiovascular diseases, and a composite genetic risk score (GRS) based on 27 single nucleotide polymorphisms (SNPs) was reported to predict risk of cardiovascular events in the general population. We aimed to evaluate this risk score in renal transplant recipients, a population with heightened cardiovascular risk, with a yet unknown genetic contribution. A total of 1640 participants from the ALERT trial (Assessment of Lescol in Renal Transplantation), a study comparing fluvastatin with placebo in stable renal transplant recipients, were genotyped for all SNPs making up the GRS. Risk alleles were weighted by the log of odds ratios reported in genome wide association studies and summed. Associations between GRS and time from study inclusion to first major cardiovascular event (MACE) were analyzed by Cox regression. In analyses adjusted for cardiovascular risk factors, GRS was significantly associated with MACE (hazard ratio [HR] 1.81, P = .006) when comparing genetic high-risk patients (quartile 4) with genetic low-risk participants (quartile 1). A 27-SNP GRS, which predicted cardiovascular events in the nontransplant population, appears to have predictive value also in kidney allograft recipients. Refining the score to better fit the transplant population seems feasible.

Genome-wide association identifies methane production level relation to genetic control of digestive tract development in dairy cows

The global temperatures are increasing. This increase is partly due to methane (CH4) production from ruminants, including dairy cattle. Recent studies on dairy cattle have revealed the existence of a heritable variation in CH4 production that enables mitigation strategies based on selective breeding. We have exploited the available heritable variation to study the genetic architecture of CH4 production and detected genomic regions affecting CH4 production. Although the detected regions explained only a small proportion of the heritable variance, we showed that potential QTL regions affecting CH4 production were located within QTLs related to feed efficiency, milk-related traits, body size and health status. Five candidate genes were found: CYP51A1 on BTA 4, PPP1R16B on BTA 13, and NTHL1, TSC2, and PKD1 on BTA 25. These candidate genes were involved in a number of metabolic processes that are possibly related to CH4 production. One of the most promising candidate genes (PKD1) was related to the development of the digestive tract. The results indicate that CH4 production is a highly polygenic trait.

Heritability of methane emissions from dairy cows over a lactation measured on commercial farms

Methane emission is currently an important trait in studies on ruminants due to its environmental and economic impact. Recent studies were based on short-time measurements on individual cows. As methane emission is a longitudinal trait, it is important to investigate its changes over a full lactation. In this study, we aimed to estimate the heritability of the estimated methane emissions from dairy cows using Fourier-transform infrared spectroscopy during milking in an automated milking system by implementing the random regression method. The methane measurements were taken on 485 Polish Holstein-Friesian cows at 2 commercial farms located in western Poland. The overall daily estimated methane emission was 279 g/d. Genetic variance fluctuated over the course of lactation around the average level of 1,509 (g/d), with the highest level, 1,866 (g/d), at the end of the lactation. The permanent environment variance values started at 2,865 (g/d) and then dropped to around 846 (g/d) at 100 d in milk (DIM) to reach the level of 2,444 (g/d) at the end of lactation. The residual variance was estimated at 2,620 (g/d). The average repeatability was 0.25. The heritability level fluctuated over the course of lactation, starting at 0.23 (SE 0.12) and then increasing to its maximum value of 0.3 (SE 0.08) at 212 DIM and ending at the level of 0.27 (SE 0.12). Average heritability was 0.27 (average SE 0.09). We have shown that estimated methane emission is a heritable trait and that the heritability level changes over the course of lactation. The observed changes and low genetic correlations between distant DIM suggest that it may be important to consider the period in which methane phenotypes are collected.

Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling

Psoriasis is a common inflammatory skin disorder for which multiple genetic susceptibility loci have been identified, but few resolved to specific functional variants. In this study, we sought to identify common and rare psoriasis-associated gene-centric variation. Using exome arrays we genotyped four independent cohorts, totalling 11 861 psoriasis cases and 28 610 controls, aggregating the dataset through statistical meta-analysis. Single variant analysis detected a previously unreported risk locus at TNFSF15 (rs6478108; P = 1.50 × 10-8, OR = 1.10), and association of common protein-altering variants at 11 loci previously implicated in psoriasis susceptibility. We validate previous reports of protective low-frequency protein-altering variants within IFIH1 (encoding an innate antiviral receptor) and TYK2 (encoding a Janus kinase), in each case establishing a further series of protective rare variants (minor allele frequency < 0.01) via gene-wide aggregation testing (IFIH1: pburden = 2.53 × 10-7, OR = 0.707; TYK2: pburden = 6.17 × 10-4, OR = 0.744). Both genes play significant roles in type I interferon (IFN) production and signalling. Several of the protective rare and low-frequency variants in IFIH1 and TYK2 disrupt conserved protein domains, highlighting potential mechanisms through which their effect may be exerted.

HLA haplotypes in primary sclerosing cholangitis patients of admixed and non-European ancestry

Primary sclerosing cholangitis (PSC) is strongly associated with several human leukocyte antigen (HLA) haplotypes. Due to extensive linkage disequilibrium and multiple polymorphic candidate genes in the HLA complex, identifying the alleles responsible for these associations has proven difficult. We aimed to evaluate whether studying populations of admixed or non-European descent could help in defining the causative HLA alleles. When assessing haplotypes carrying HLA-DRB1*13:01 (hypothesized to specifically increase the susceptibility to chronic cholangitis), we observed that every haplotype in the Scandinavian PSC population carried HLA-DQB1*06:03. In contrast, only 65% of HLA-DRB1*13:01 haplotypes in an admixed/non-European PSC population carried this allele, suggesting that further assessments of the PSC-associated haplotype HLA-DRB1*13:01-DQA1*01:03-DQB1*06:03 in admixed or multi-ethnic populations could aid in identifying the causative allele.

Large scale meta-analysis characterizes genetic architecture for common psoriasis associated variants

Psoriasis is a complex disease of skin with a prevalence of about 2%. We conducted the largest meta-analysis of genome-wide association studies (GWAS) for psoriasis to date, including data from eight different Caucasian cohorts, with a combined effective sample size >39,000 individuals. We identified 16 additional psoriasis susceptibility loci achieving genome-wide significance, increasing the number of identified loci to 63 for European-origin individuals. Functional analysis highlighted the roles of interferon signalling and the NFκB cascade, and we showed that the psoriasis signals are enriched in regulatory elements from different T cells (CD8⁺ T-cells and CD4⁺ T-cells including T_H0, T_H1 and T_H17). The identified loci explain ∼28% of the genetic heritability and generate a discriminatory genetic risk score (AUC=0.76 in our sample) that is significantly correlated with age at onset (p=2 × 10^-89). This study provides a comprehensive layout for the genetic architecture of common variants for psoriasis.

CD4+ T cells from patients with primary sclerosing cholangitis exhibit reduced apoptosis and down-regulation of proapoptotic Bim in peripheral blood

The pathogenesis of the progressive liver disease, primary sclerosing cholangitis (PSC), remains largely elusive. The strong genetic association with HLA loci suggests that T cell–dependent, adaptive immune reactions could contribute to disease pathogenesis. Recent studies have indicated that PSC is also associated with polymorphisms in the locus encoding for proapoptotic Bim (BCL2L11). Bim is crucial for the maintenance of immunologic tolerance through induction of apoptosis in activated T cells. Of interest with regard to PSC is the finding that BCL2L11-deficient mice develop periductular infiltrates. We, therefore, investigated, whether defective apoptosis of T cells might contribute to the phenotype of PSC. Thus, we induced apoptosis of T cells from patients with PSC and controls by repeated T cell receptor (TCR) stimulation or cytokine withdrawal. We found that CD4+ T cells, but not CD8+ T cells, from patients with PSC exhibited significantly reduced apoptosis in response to both, TCR restimulation or cytokine withdrawal. This increased apoptosis resistance was associated with significantly reduced up-regulation of proapoptotic Bim in T cells from patients with PSC. However, T cell apoptosis did not seem to be influenced by the previously described BCL2L11 polymorphisms. Reduced CD4+ T cell apoptosis in patients with PSC was not due to reduced cell activation, as indicated by a similar surface expression of the activation markers CD69, CD25, and CD28 in T cells from patients and controls. Thus, decreased apoptosis of activated CD4+ T cells may be part of the immune dysregulation observed in patients with PSC.

Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease

Primary sclerosing cholangitis (PSC) is a rare progressive disorder leading to bile duct destruction; ∼75% of patients have comorbid inflammatory bowel disease (IBD). We undertook the largest genome-wide association study of PSC (4,796 cases and 19,955 population controls) and identified four new genome-wide significant loci. The most associated SNP at one locus affects splicing and expression of UBASH3A, with the protective allele (C) predicted to cause nonstop-mediated mRNA decay and lower expression of UBASH3A. Further analyses based on common variants suggested that the genome-wide genetic correlation (r_G) between PSC and ulcerative colitis (UC) (r_G = 0.29) was significantly greater than that between PSC and Crohn's disease (CD) (r_G = 0.04) (P = 2.55 × 10^-15). UC and CD were genetically more similar to each other (r_G = 0.56) than either was to PSC (P < 1.0 × 10^-15). Our study represents a substantial advance in understanding of the genetics of PSC.

Single Nucleotide Polymorphisms and Long-Term Clinical Outcome in Renal Transplant Patients: A Validation Study

Genome-wide association studies (GWAS) are designed to investigate single nucleotide polymorphisms (SNPs) and the association with a clinical phenotype. A previous GWAS performed in 300 renal transplant recipients identified two SNPs (rs3811321 and rs6565887) associated with serum creatinine and clinical outcome. We sought to validate these findings. Genotyping of the two SNPs was performed using Taqman assays in 1638 Caucasians participating in the Assessment of LEscol in Renal Transplant (ALERT) study. Primary endpoint was death-censored graft loss, and secondary endpoint was all-cause mortality. Applying Cox regression, no crude association to graft loss was found for rs3811321 on chromosome 14 (hazard ratio [HR] 0.87, 95% CI 0.59-1.29, p = 0.50) or rs6565887 on chromosome 18 (HR 0.88, CI 0.62-1.25, p = 0.48). Multivariable adjustments did not change results, nor did evaluation of the number of risk alleles formed by the two SNPs. No association with mortality was detected. In conclusion, an impact of two SNPs on chromosomes 14 and 18 on death-censored graft survival or all-cause mortality was not confirmed. Our results emphasize the importance of validating findings from high-throughput genetics studies and call for large collaborative research initiatives in the field of transplantation outcomes.

A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis

Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. Through replication genotyping and imputation we found that a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis (overall P=6.89 × 10(-7), odds ratio=0.30). We further demonstrate that the truncated protein exhibits reduced expression and altered subcellular localization, suggesting the protective mechanism may reside in the loss of an interaction or function via mislocalization and/or loss of an essential transmembrane domain.

Rates of inbreeding and genetic adaptation for populations managed as herds in zoos with a rotational mating system or with optimized contribution of parents

This study compares two genetic management scenarios for species kept in herds, such as deer. The simulations were designed so that their results can be extended to a wide range of zoo populations. In the first scenario, the simulated populations of size 3 × 20, 6 × 40 or 20 × 60 (herds × animals in herd) were managed with a rotational mating (RM) scheme in which 10%, 20% or 50% of males were selected for breeding and moved between herds in a circular fashion. The second scenario was based on optimal contribution theory (OC). OC requires an accurate pedigree to calculate kinship; males were selected and assigned numbers of offspring to minimize kinship in the next generation. RM was efficient in restriction of inbreeding and produced results comparable with OC. However, RM can result in genetic adaptation of the population to the zoo environment, in particular when 20% or less males are selected for rotation and selection of animals is not random. Lowest rates of inbreeding were obtained by combining OC with rotation of males as in the RM scheme. RM is easy to implement in practice and does not require pedigree data. When full pedigree is available, OC management is preferable.

Genetic diversity in Hucul and Polish primitive horse breeds

Abstract. Pedigree and molecular data were used to evaluate genetic diversity in the Polish populations of the Polish primitive horse (also known as Polish Konik) and Hucul breeds over the time period of 30 years (1980–2011). Based on genotypes in 12 microsatellite loci (for 3865 Polish primitive horses and 1627 Huculs), as well as on pedigree data derived from over 7000 individuals (both breeds), several indices describing structure of the analysed populations were estimated. For both analysed breeds, we observed an increasing trend of inbreeding since 1980 which seems to be much more stable (oscillating around 10 % in the Polish primitive horse and 5 % in Hucul) since the beginning of 2000s when they were included in conservation programs in Poland. We observed that generally, indices related to genetic diversity are higher in the Hucul breed. Our study indicated that genetic diversity in the Polish primitive horse and Hucul breeds in Poland is still relatively high and conservation programs should be continued to keep it on the "safe" level in the future.

Genetic analysis of milk urea nitrogen and relationships with yield and fertility across lactation

The aim of this project was to investigate the relationship of milk urea nitrogen (MUN) with 3 milk production traits [milk yield (MY), fat yield (FY), protein yield (PY)] and 6 fertility measures (number of inseminations, calving interval, interval from calving to first insemination, interval from calving to last insemination, interval from first to last insemination, and pregnancy at first insemination). Data consisted of 635,289 test-day records of MY, FY, PY, and MUN on 76,959 first-lactation Swedish Holstein cows calving from 2001 to 2003, and corresponding lactation records for the fertility traits. Yields and MUN were analyzed with a random regression model followed by a multi-trait model in which the lactation was broken into 10 monthly periods. Heritability for MUN was stable across lactation (between 0.16 and 0.18), whereas MY, FY, and PY had low heritability at the beginning of lactation, which increased with time and stabilized after 100 d in milk, at 0.47, 0.36, and 0.44, respectively. Fertility traits had low heritabilities (0.02 to 0.05). Phenotypic correlations of MUN and milk production traits were between 0.13 (beginning of lactation) and 0.00 (end of lactation). Genetic correlations of MUN and MY, FY, and PY followed similar trends and were positive (0.22) at the beginning and negative (-0.15) at the end of lactation. Phenotypic correlations of MUN and fertility were close to zero. A surprising result was that genetic correlations of MUN and fertility traits suggest a positive relationship between the 2 traits for most of the lactation, indicating that animals with breeding values for increased MUN also had breeding values for improved fertility. This result was obtained with a random regression model as well as with a multi-trait model. The analyzed group of cows had a moderate level of MUN concentration. In such a population MUN concentration may increase slightly due to selection for improved fertility. Conversely, selection for increased MUN concentration may improve fertility slightly.

Expression of p65 gene in experimental colon cancer under the influence of 5-fluorouracil given alone and in combination with hormonal modulation

The effect of tamoxifen (TAM), lanreotide (LAN) and 5-fluorouracil (5-FU), given separately or together, on p65 gene expression in murine Colon 38 cancer was investigated by RT-PCR method. The findings were compared with cell proliferation determined by bromodeoxyuridine (BrdU) labeling index, apoptosis visualized by TUNEL method and tumor mass. It was found that in the control group (mice bearing colon cancer without treatment) the expression of p65 gene was present in 57% of investigated samples. In the groups treated with TAM or LAN p65 gene expression was detected in 87.5% and 83.3% of analyzed cases, respectively. Both these substances increased apoptotic index in Colon 38 cancer and LAN also decreased the proliferation index. After a combined treatment with TAM and LAN a percentage of p65 positive cases was similar to that of the control group and equaled approximately 60%. This treatment did not increase proapoptotic effects of these drugs, and even reduced the antiproliferogenic effect of LAN. In the group treated with 5-FU and LAN p65 gene expression was also close to the control value (about 66%). Similarly in this group the combined treatment with these two drugs did not cause any favorable effect on proliferation and apoptosis. Moreover, in this group even reduced antiproliferogenic effect of LAN was observed. In the group with 5-FU alone the expression of p65 was present in about 80% of samples. The treatment with 5-FU increased apoptotic index and did not change proliferation. In the group treated with a combination of TAM and 5-FU all analyzed cases showed the presence of p65 gene expression. Previously, we observed in this group the most pronounced and synergistic effect of these substances on the inhibition of cell proliferation and tumor mass reduction. Based on these findings we conclude that p65 gene expression in murine Colon 38 cancer tissues can be modulated via chemotherapy (5-FU) and also via hormonal modulation (TAM and LAN).

The involvement of angiotensins in the control of prostatic epithelial cell proliferation in the rat

The effects of captopril (the inhibitor of the angiotensin-converting enzyme) and of angiotensins II and IV (3-8 fragment of angiotensin II) on cell proliferation of the prostatic epithelium was investigated in the rat. The incorporation of bromodeoxyuridine into cell nuclei was used as an index of cell proliferation. It was found that the treatment with captopril resulted in the suppression of prostatic epithelial cell proliferation. The antiproliferative effect of captopril was reversed (at least partially) by a simultaneous treatment with either angiotensin II or angiotensin IV. The effects of angiotensins were not blocked by the administration of losartan--AT1 angiotensin receptor blocker. These findings suggest the involvement of angiotensins in the control of prostatic growth, acting via the receptors different from the AT1-subtype (presumably via AT4 receptors).

Angiotensins II and IV stimulate the rat adrenocortical cell proliferation acting via different receptors

OBJECTIVE

The effects of angiotensins II (Ang II) and IV (Ang IV,3-8 fragment of angiotensin II) on the adrenocortical cell proliferation have been investigated in the rat.

METHODS

The male adult Wistar rats were injected subcutaneously with saline, captopril or captopril together with either Ang II or Ang IV. A part of animals received additionally losartan - an antagonist of AT1 subtype of angiotensin receptors. Bromodeoxyuridine (BrDU) incorporation into cell nuclei was used as the index of cell proliferation.

RESULTS

It was found that both Ang II and Ang IV increased the BrDU labeling in the adrenal cortex of captopril-pretreated rats. This effect involved mainly the zona glomerulosa cells. The proliferogenic effect of Ang II was blocked by AT1 receptor antagonist losartan. In contrast, losartan did not block the effect of Ang IV.

CONCLUSION

Both Ang II and Ang IV stimulate the adrenocortical cell proliferation in the rat, but they act via different receptors - AT1 in the case of Ang II and non-AT1 (probably AT4) in the case of Ang IV.

Diabetic ketoacidosis in a patient with acromegaly

Abnormalities of glucose metabolism are a common feature of acromegaly. Overt diabetes mellitus develops in about 10-15% of patients. We present an unusual complication of acromegaly: a 37-year old man with a 2-year history of acromegaly developed diabetic ketoacidosis 3 weeks after transsphenoidal adenomectomy. No specific cause for this sudden metabolic derangement could be demonstrated. Insulin need was very high in the first days after the onset of ketoacidosis, but was considerably reduced after initiation of treatment with octreotide and after successful re-operation.

Pituitary-adrenocortical responses to the chronic administration of granulocyte colony-stimulating factor in rats

Granulocyte colony-stimulating factor (G-CSF) is a hematopoietic growth factor, but it may play a role in the regulation of the neuroendocrine system activity. Only few data are available about its possible influence on the pituitary gland. We have recently reported an acute stimulatory effect of G-CSF (and of GM-CSF) on adrenocorticotropic hormone (ACTH) secretion in rats in vivo. The purpose of the present study was to evaluate whether chronic administration of G-CSF affects ACTH and corticosterone secretion and growth processes of the rat anterior pituitary gland and adrenal cortex in vivo. We have demonstrated that G-CSF (at a dose of 10.0 microg/kg body weight (BW)) injected s.c. once daily (for 7 days), stimulated both ACTH and corticosterone secretion. Simultaneously, G-CSF treatment did not change the total anterior pituitary cell proliferation as revealed by immunohistochemical staining of proliferating cell nuclear antigen (PCNA). On the other hand, proliferative activity of corticotrophs, detected in the sections of the anterior pituitary using double-labeling. was significantly increased after treatment with G-CSF. Moreover, this growth factor induced an increase in the proliferation ratio in the entire adrenal equatorial section. These findings suggest an involvement of G-CSF in the regulation of pituitary-adrenal axis and support the hypothesis of bidirectional associations between the immune system and the endocrine glands.

Influence of granulocyte-macrophage colony stimulating factor on pituitary-adrenal axis (PAA) in rats in vivo

We have studied the in vivo influence of granulocyte-macrophage colony stimulating factor (GM-CSF) on blood plasma concentration of adrenocorticotropic hormone (ACTH) and corticosterone in Wistar rats. The administration of 10 micrograms/kg b.w. GM-CSF at 45 (P < 0.01), 90 (P < 0.01) and at 45 (P < 0.001), 90 (P < 0.001) and 180 min (P < 0.001) increased the secretion of ACTH and corticosterone, respectively. Prolonged administration of 10 micrograms/kg b.w. of GM-CSF increased the ACTH (P < 0.001) and corticosterone (P < 0.001) concentration in blood plasma. We have also found that chronic treatment with 10 micrograms/kg b.w. of GM-CSF increased the proliferative activity of corticotrophs (P < 0.05), but it did not significantly change the total cell proliferation in the anterior pituitary gland. Moreover, this cytokine increased cell proliferation of the adrenal cortex (P < 0.001). These experiments suggest that GM-CSF activates the pituitary-adrenal axis and support the hypothesis of bidirectional associations between the immune and neuroendocrine systems.

The involvement of the renin-angiotensin system in the regulation of cell proliferation in the rat endometrium

Oestrogens are known to enhance angiotensin biosynthesis by increasing the elaboration of its precursor, angiotensinogen. On the other hand, we found that inhibition of angiotensin-converting enzyme (ACE) suppressed the proliferative response of the rat anterior pituitary gland to oestrogens. To answer the question whether the angiotensin system is involved in the control of the cell proliferation of the uterine epithelium, the effects of an ACE inhibitor, enalapril maleate, and of angiotensins II and IV, alone or together with losartan, an antagonist of angiotensin receptor type 1 (AT1), on endometrial epithelial cell proliferation have been studied. The experiments were performed on ovariectomized female Wistar rats. In the first experiment the animals were injected with a single dose of oestradiol benzoate or received an injection of solvent only. Half of the oestrogen-treated rats were injected additionally with enalapril maleate (EN, twice daily). The incorporation of bromodeoxyuridine (BrDU) into endometrial cell nuclei was used as an index of cell proliferation. It was found that oestradiol alone dramatically increased the BrDU labelling index (LI) of endometrial cell nuclei, and this effect was partially blocked by the simultaneous treatment with EN. In the second experiment, the animals were injected intraperitoneally with angiotensin II (AII), angiotensin IV (AIV) or saline, alone or together with losartan. It was found that AIV induced an increase in the LI in uterine epithelium, and this effect was not blocked by the simultaneous treatment with losartan. The increase in LI in uterine epithelium was also observed in the rats treated with AII and with losartan. These findings suggest an involvement of angiotensin IV in the control of uterine epithelium cell proliferation.

The effect of angiotensin II receptor antagonists on diethylstilbestrol-induced vascular changes in the rat anterior pituitary gland: a quantitative evaluation

The effects if diethylstilbestrol (DES) and of angiotensin II (Ang II) receptor antagonists, such as losartan (selective AT1 receptor antagonist) or PD 123319 (selective AT2 receptor antagonist) on the anterior pituitary microvasculature were studied by means of computer-assisted image analysis. The vascularization was visualized using Selye's method modified by Poely et al. (1964). It was found that DES induced a sharp increase in vessel area, mean vessel diameter and perimeter, whereas mean vessel number was reduced. These DES-induced changes were inhibited by simultaneous administration of losartan. On the other hand, PD 123319 was less effective. These findings suggest an involvement of Ang II, acting mainly via AT1 receptors, in the mechanism of estrogen-induced vascular changes in the rat anterior pituitary gland.

Inhibitory effects of fumagillin and its analogue TNP-470 on the function, morphology and angiogenesis of an oestrogen-induced prolactinoma in Fischer 344 rats

The process of angiogenesis occurs in many physiological states, but it is also essential for the growth of solid tumours and metastasis formation. An abnormal arterial vascularization has been shown in prolactin-secreting pituitary adenomas induced by prolonged treatment with oestrogens in Fischer 344 (F344) rats. It is thought that anti-angiogenic agents might be useful in therapy for these tumours. Fumagillin and its analogue TNP-470 are known to inhibit endothelial cell proliferation selectively, but their effect on lactotroph cell secretory function and prolactinoma formation has not yet been described. The aim of the present study was to examine the effects of fumagillin and TNP-470 on prolactin secretion, and morphological and vascular changes within the anterior pituitary in long-term oestrogen-treated male F344 rats in vivo and in vitro. As expected, 7 weeks after s.c. implantation of Silastic tubes containing 10 mg diethyl-stilboestrol (DES), a very high rise in serum prolactin levels was found. Both angiogenesis inhibitors injected s.c. at doses of 10 mg/kg body weight for 24 days attenuated the stimulatory effect of DES on prolactin production and release. They also diminished prolactin cell density and inhibited cell proliferation expressed as the number of anterior pituitary cells labelled with bromodeoxyuridine (BrdU), but the effect of TNP-470 was minor compared with fumagillin. Both angioinhibitors suppressed neo-vascularization within the anterior pituitary with similar potency but, on the other hand, they did not affect DES-induced increases in prolactin secretion from cultured rat pituitary cells and cell proliferation in vitro. In conclusion, our results provide strong evidence for the anti-tumour and anti-prolactin activity of angiogenesis inhibitors in the experimentally oestrogen-induced pituitary adenoma; this might be mediated indirectly through the inhibition of angiogenesis.

Effect of granulocyte-macrophage colony stimulating factor and granulocyte colony stimulating factor on prolactin and adrenocorticotropic hormone secretion in rats: dose- and time-response in vivo studies

The in vivo effect of granulocyte-macrophage colony stimulating factor (GM-CSF) and granulocyte colony stimulating factor (G-CSF) on the plasma levels of prolactin (PRL) and adrenocorticotropic hormone (ACTH) in rats were studied. The administration of 10 micrograms/kg G-CSF at 45 min (p < 0.05) and 90 min (p < 0.01) or 10 micrograms/kg GM-CSF at 45 and 90 min (p < 0.01) stimulated the secretion of ACTH. Moreover, G-CSF administration only, in doses of 10 micrograms/kg at 45 min (p < 0.05) and 90 min (p < 0.01) augmented PRL secretion into the blood. These experiments suggest that the human colony stimulating factors (GM-CSF and G-CSF) activate the anterior pituitary gland in vivo to ACTH secretion, but only G-CSF positively influenced PRL release in rats.

Effect of granulocyte-macrophage colony stimulating factor and granulocyte colony stimulating factor on melatonin secretion in rats in vivo and in vitro studies

The study was performed in order to clarify whether granulocyte-macrophage colony stimulating factor (GM-CSF) and granulocyte colony stimulating factor (G-CSF) affect melatonin production and release. We have found that both factors (GM-CSF at doses of 10.0 and 100.0 micrograms/kg, and G-CSF at doses of 1.0, 10.0, and 100.0 micrograms/kg) stimulate melatonin secretion in rats in vivo. Positive correlations between tested doses of GM-CSF and G-CSF and plasma melatonin levels were observed (P < 0.01). Moreover, GM-CSF at doses of 2.0 and 20.0 ng/ml activated in vitro the pineal gland to melatonin release (P < 0.05) in a dose-dependent manner.

Influence of interleukin 1 and antihuman interleukin 1 receptor antibody on the growth and function of the thyroid gland in rats

Cytokines seem to influence the hypothalamo-pituitary-thyroid axis. We have studied the effect of different doses of interleukin 1 alpha (IL-1 alpha) and IL-1 beta (given twice daily ip) alone or together with antihuman IL-1 receptor antibody (aIL-1ra) on the proliferation of thyroid follicular cells and thyroid hormone levels in male Wistar rats. We have examined the influence of IL-1 alpha and IL-1 beta at doses of 10.0, 1.0 and 0.1 micrograms/kg body wt of animal and aIL-1ra at a dose of 10.0 micrograms/kg body wt of animals. The incorporation of bromodeoxyuridine into thyroid follicular cell nuclei was used as an index of cell proliferation (labeling index: LI) and measured 24 h after the last of two injections of interleukin. Interleukin 1 beta, at all examined doses, increased thyroid follicular cell proliferation when compared to controls (p < 0.05), and a positive correlation between log of the dose of IL-1 beta used and LI (r = 0.62, p < 0.05) using Student's t-test was found. The administration of aIL-1ra alone also enhanced the thyroid follicular cell proliferation, whereas aIL-1ra used together with IL-1 beta exerted a less pronounced effect than each of these substances used separately (p < 0.05). Interleukin 1 alpha at the dose of 10.0 micrograms/kg body wt increased the proliferation of thyroid follicular cells (p < 0.05). Thyroid hormone levels did not change in any of the experiments. These results suggest a regulatory role of IL-1 upon the proliferation of thyroid cells.

Interleukin-1 beta stimulates cell proliferation in the intermediate lobe of the rat pituitary gland

Interleukin-1 (IL-1) is a multifunctional monokine which possesses an impressive array of diverse actions relating to the function of the immune system. IL-1 is present and formed locally in the brain as demonstrated by biochemical and immunocytochemical methods. Various immunomodulatory and neuroendocrine effects of IL-1 have been reported, including induction of several morphological changes in the endocrine cells of experimental animals and humans. IL-1 is present in two molecular forms (IL-1 alpha and IL-1 beta) that activate specific receptors for IL-1. In the present study we investigated the possible effect of recombinant human IL-1 alpha and IL-1 beta and recently cloned anti-human IL-1 receptor antibody (M10) on cell proliferation in the anterior and the intermediate lobe of the pituitary gland of the rat. In vivo labelling with bromodeoxyuridine (BrdU) and immunocytochemical staining with anti-BrdU monoclonal antibody were used as a sensitive index of cell proliferation. IL-1 beta was found to stimulate dose-dependently (0.1-10 micrograms/kg body weight) incorporation of BrdU into pituitary intermediate cell nuclei, and positive correlation between the tested doses of IL-1 beta and BrdU-labelling index was noted (r = 0.89; P < 0.01). This IL-1 beta-induced stimulation of pituitary pars intermedia cell proliferation was receptor specific, since stimulation was blocked by anti-IL-1 receptor antibody. On the other hand, recombinant human IL-1 alpha did not affect BrdU incorporation and the proliferation of pituitary pars intermedia cells.(ABSTRACT TRUNCATED AT 250 WORDS)