Genetics of colitis susceptibility in IL-10-deficient mice: backcross versus F2 results contrasted by principal component analysis

Multivariate genome-wide associations for immune traits in two maternal pig lines

BACKGROUND

Immune traits are considered to serve as potential biomarkers for pig's health. Medium to high heritabilities have been observed for some of the immune traits suggesting genetic variability of these phenotypes. Consideration of previously established genetic correlations between immune traits can be used to identify pleiotropic genetic markers. Therefore, genome-wide association study (GWAS) approaches are required to explore the joint genetic foundation for health biomarkers. Usually, GWAS explores phenotypes in a univariate (uv), trait-by-trait manner. Besides two uv GWAS methods, four multivariate (mv) GWAS approaches were applied on combinations out of 22 immune traits for Landrace (LR) and Large White (LW) pig lines.

RESULTS

In total 433 (LR: 351, LW: 82) associations were identified with the uv approach implemented in PLINK and a Bayesian linear regression uv approach (BIMBAM) software. Single Nucleotide Polymorphisms (SNPs) that were identified with both uv approaches (n = 32) were mostly associated with immune traits such as haptoglobin, red blood cell characteristics and cytokines, and were located in protein-coding genes. Mv GWAS approaches detected 647 associations for different mv immune trait combinations which were summarized to 133 Quantitative Trait Loci (QTL). SNPs for different trait combinations (n = 66) were detected with more than one mv method. Most of these SNPs are associated with red blood cell related immune trait combinations. Functional annotation of these QTL revealed 453 immune-relevant protein-coding genes. With uv methods shared markers were not observed between the breeds, whereas mv approaches were able to detect two conjoint SNPs for LR and LW. Due to unmapped positions for these markers, their functional annotation was not clarified.

CONCLUSIONS

This study evaluated the joint genetic background of immune traits in LR and LW piglets through the application of various uv and mv GWAS approaches. In comparison to uv methods, mv methodologies identified more significant associations, which might reflect the pleiotropic background of the immune system more accurately. In genetic research of complex traits, the SNP effects are generally small. Furthermore, one genetic variant can affect several correlated immune traits at the same time, termed pleiotropy. As mv GWAS methods consider strong dependencies among traits, the power to detect SNPs can be boosted. Both methods revealed immune-relevant potential candidate genes. Our results indicate that one single test is not able to detect all the different types of genetic effects in the most powerful manner and therefore, the methods should be applied complementary.

Persistence of Lgr5+ colonic epithelial stem cells in mouse models of inflammatory bowel disease

Intestinal mucosal healing is the primary therapeutic goal of medical treatments for inflammatory bowel disease (IBD). Epithelial stem cells are key players in the healing process. Lgr5+ stem cells maintain cellular turnover during homeostasis in the colonic crypt. However, they are lost and dispensable for repair in a wide variety of injury models, including dextran sulfate sodium (DSS) colitis, radiation, helminth infection, and T-cell activation. The direct loss of Lgr5+ cells activates a plasticity response in the epithelium in which other cell types can serve as stem cells. Whether this paradigm applies to mouse models of IBD remains unknown. In contrast to previously tested models, IBD models involve an inflammatory response rooted in the loss of immunologic tolerance to intestinal luminal contents including the microbiome. Here, we show the persistence of Lgr5+ cells in oxazolone, 2,4,6-trinitrobenzene sulfonic acid (TNBS), and Il10^-/-, and Il10^-/- Tnfr1^-/- IBD models. This contrasts with results obtained from DSS-induced injury. Through high-throughput expression profiling, we find that these colitis models were associated with distinct patterns of cytokine expression. Direct exposure of colonic epithelial organoids to DSS, oxazolone, or TNBS resulted in increased apoptosis and loss of Lgr5+ cells. Targeted ablation of Lgr5+ cells resulted in severe exacerbation of chronic, antibody-induced IL-10-deficient colitis, but had only modest effects in TNBS-induced colitis. These results show that distinct mouse models of IBD-like colitis induce different patterns of Lgr5+ stem cell retention and function.NEW & NOTEWORTHY Acute intestinal injury and epithelial repair are associated with the loss of fast-cycling Lgr5+ stem cells and plasticity in the activation of formerly quiescent cell populations. In contrast, here we show in murine inflammatory bowel disease the persistence of the Lgr5+ stem cell population and its essential role in restricting the severity of chronic colitis. This demonstrates a diversity of stem cell responses to colitis.

Role of MicroRNA in Inflammatory Bowel Disease: Clinical Evidence and the Development of Preclinical Animal Models

The dysregulation of microRNA (miRNA) is implicated in cancer, inflammation, cardiovascular disorders, drug resistance, and aging. While most researchers study miRNA's role as a biomarker, for example, to distinguish between various sub-forms or stages of a given disease of interest, research is also ongoing to utilize these small nucleic acids as therapeutics. An example of a common pleiotropic disease that could benefit from miRNA-based therapeutics is inflammatory bowel disease (IBD), which is characterized by chronic inflammation of the small and large intestines. Due to complex interactions between multiple factors in the etiology of IBD, development of therapies that effectively maintain remission for this disease is a significant challenge. In this review, we discuss the role of dysregulated miRNA expression in the context of clinical ulcerative colitis (UC) and Crohn's disease (CD)-the two main forms of IBD-and the various preclinical mouse models of IBD utilized to validate the therapeutic potential of targeting these miRNA. Additionally, we highlight advances in the development of genetically engineered animal models that recapitulate clinical miRNA expression and provide powerful preclinical models to assess the diagnostic and therapeutic promise of miRNA in IBD.

IL-10 Receptor Neutralization-Induced Colitis in Mice: A Comprehensive Guide

Interleukin-10 (IL-10) and its receptor (IL-10R) have been foremost targets to understand inflammatory bowel disease (IBD) pathogenesis. For the past several decades, IL-10-deficient (Il10^-/- ) mice were considered one of the best models to study immune-mediated colitis. Several physiologic limitations with this model, e.g., delayed and varied disease onset, have hindered investigators in testing new clinical therapies for IBD. In this article, we provide comprehensive guidance for using anti-IL-10R monoclonal antibody (αIL-10R mAb) neutralization as a superior alternative model to study IBD. This article describes the feasibility of using αIL-10R mAb to induce chronic colitis (within 4 weeks), perform time-dependent mechanistic studies, and assess the efficacy of IBD therapeutics. This article also delineates protocols for in-house assays to critically assess colitis and associated inflammatory parameters. Overall, we underscore αIL-10R mAb neutralization as a relevant immune-mediated murine colitis model to study human Crohn's disease. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Induction of chronic colitis in mice via αIL-10R mAb neutralization Basic Protocol 2: Biochemical evaluation of αIL-10R mAb neutralization-induced chronic colitis Support Protocol 1: Stool analysis and scoring Support Protocol 2: Swiss roll method.

TNF Receptor 1 Promotes Early-Life Immunity and Protects against Colitis in Mice

Neutralization of tumor necrosis factor (TNF) represents a widely used therapeutic strategy for autoimmune diseases including inflammatory bowel disease (IBD). However, the fact that many patients with IBD are non-responsive to anti-TNF therapies suggests the need for a better understanding of TNF signaling in IBD. Here, we show that co-deletion of TNF receptor 1 (TNFR1, Tnfrsf1a) in the Il10^-/- spontaneous colitis model exacerbates disease, resulting in very-early-onset inflammation after weaning. The disease can be interrupted by treatment with antibiotics. The single deletion of TNFR1 induces subclinical colonic epithelial dysfunction and mucosal immune abnormalities, including accumulation of neutrophils and depletion of B cells. During the pre-disease period (before weaning), both Tnfr1^-/- and Il10^-/-Tnfr1^-/- animals exhibit impaired expression of pro-inflammatory cytokines compared with wild-type and Il10^-/- controls, respectively. Collectively, these results demonstrate the net anti-inflammatory functions of TNF/TNFR1 signaling through the regulation of colonic immune homeostasis in early life.

CD14 and ALPK1 Affect Expression of Tight Junction Components and Proinflammatory Mediators upon Bacterial Stimulation in a Colonic 3D Organoid Model

Cd14 and Alpk1 both encode pathogen recognition receptors and are known candidate genes for affecting severity in inflammatory bowel diseases. CD14 acts as a coreceptor for bacterial lipopolysaccharide (LPS), while ALPK1 senses ADP-D-glycero-beta-D-manno-heptose, a metabolic intermediate of LPS biosynthesis. Intestinal barrier integrity can be influenced by CD14, whereas to date, the role of ALPK1 in maintaining barrier function remains unknown. We used colon-derived 3D organoids, first characterised for growth, proliferation, stem cell markers, and expression of tight junction (TJ) components using qPCR and immunohistochemistry. They showed characteristic crypt stem cells, apical shedding of dead cells, and TJ formation. Afterwards, organoids of different genotypes (WT, Il10^−/−, Cd14^−/−, and Alpk1^−/−) were then stimulated with either LPS or Escherichia coli Nissle 1917 (EcN). Gene expression and protein levels of cytokines and TJ components were analysed. WT organoids increased expression of Tnfα and tight junction components. Cd14^−/− organoids expressed significantly less Tnfα and Ocln after LPS stimulation than WT organoids but reacted similarly to WT organoids after EcN stimulation. In contrast, compared to WT, Alpk1^−/− organoids showed decreased expression of different TJ and cytokine genes in response to EcN but not LPS. However, Western blotting revealed an effect of ALPK1 on TJ protein levels. These findings demonstrate that Cd14, but not Alpk1, alters the response to LPS stimulation in colonic epithelial cells, whereas Alpk1 is involved in the response upon bacterial challenge.

Analysis of Cdcs1 colitogenic effects in the hematopoietic compartment reveals distinct microbiome interaction and a new subcongenic interval active in T cells

Disease activity in Interleukin-10-deficient (Il10^-/-) mice, a model for IBD, depends on genetic background and microbiome composition. B6.129P2/JZtm-Il10^tm1Cgn (B6-Il10^-/-) mice are partially resistant to colitis, whereas mice carrying the Cdcs1^C3Bir haplotype on chromosome 3, B6.Cg-Il10^tm1CgnMMU3(D3Mit11-D3Mit348)/JZtm (BC-R3-Il10^-/-), are susceptible. This study was performed to clarify Cdcs1 and candidate gene effects on the colitogenic potential of hematopoietic cells using bone marrow (BM) and T-cell transfer models. Acute and chronic graft versus host reaction was excluded by high-density genotyping, in vitro and in vivo approaches. BM-chimeras were created with animals housed in two barriers (I and II) with distinct microbiota composition as identified by sequencing. BM-chimeras of all groups developed comparable moderate-to-severe colitis in Barrier I, however, in Barrier II only recipients of BC-R3-Il10^-/- BM. Subsequent adoptive T cell transfers pointed to a new subcongenic interval within Cdcs1 affecting their colitogenic potential. Transfers excluded Larp7 and Alpk1 but highlighted Ifi44 as potential candidate genes. In this model-system, colitis development after cell transfer heavily depends on microbiome, though Cdcs1 acts mainly independently in hematopoietic cells. A new subcongenic interval, provisionally named Cdcs1.4, modifies colitogenic T cell function. Within this locus, Ifi44 represents an important candidate gene for colitis expression.

Exome sequencing analysis reveals variants in primary immunodeficiency genes in patients with very early onset inflammatory bowel disease

BACKGROUND & AIMS

Very early onset inflammatory bowel disease (VEO-IBD), IBD diagnosed at 5 years of age or younger, frequently presents with a different and more severe phenotype than older-onset IBD. We investigated whether patients with VEO-IBD carry rare or novel variants in genes associated with immunodeficiencies that might contribute to disease development.

METHODS

Patients with VEO-IBD and parents (when available) were recruited from the Children's Hospital of Philadelphia from March 2013 through July 2014. We analyzed DNA from 125 patients with VEO-IBD (age, 3 wk to 4 y) and 19 parents, 4 of whom also had IBD. Exome capture was performed by Agilent SureSelect V4, and sequencing was performed using the Illumina HiSeq platform. Alignment to human genome GRCh37 was achieved followed by postprocessing and variant calling. After functional annotation, candidate variants were analyzed for change in protein function, minor allele frequency less than 0.1%, and scaled combined annotation-dependent depletion scores of 10 or less. We focused on genes associated with primary immunodeficiencies and related pathways. An additional 210 exome samples from patients with pediatric IBD (n = 45) or adult-onset Crohn's disease (n = 20) and healthy individuals (controls, n = 145) were obtained from the University of Kiel, Germany, and used as control groups.

RESULTS

Four hundred genes and regions associated with primary immunodeficiency, covering approximately 6500 coding exons totaling more than 1 Mbp of coding sequence, were selected from the whole-exome data. Our analysis showed novel and rare variants within these genes that could contribute to the development of VEO-IBD, including rare heterozygous missense variants in IL10RA and previously unidentified variants in MSH5 and CD19.

CONCLUSIONS

In an exome sequence analysis of patients with VEO-IBD and their parents, we identified variants in genes that regulate B- and T-cell functions and could contribute to pathogenesis. Our analysis could lead to the identification of previously unidentified IBD-associated variants.

A Multihit Model: Colitis Lessons from the Interleukin-10-deficient Mouse

Complex mechanisms are pulling the strings to initiate the development of inflammatory bowel disease. Current evidence indicates that an interaction of genetic susceptibilities (polymorphisms), environmental factors, and the host microbiota leads to a dysregulation of the mucosal immune system. In the past decades, the interleukin-10-deficient mouse has served as an excellent model to mirror the multifactorial nature of this disease. Here, we want to review in detail the interplay of the genetic factors, immune aspects, and especially summarize and discuss the role of the microbiota contributing to colitis development in the interleukin-10-deficient mouse model of inflammatory bowel disease as a multihit model.

Genome-wide association analyses for boar taint components and testicular traits revealed regions having pleiotropic effects

Background

The aim of this study was to perform a genome-wide association analyses (GWAS) for androstenone, skatole and indole in different Pietrain sire lines and compare the results with previous findings in purebred populations. Furthermore, the genetic relationship of androstenone and skatole were investigated with respect to pleiotropy. In order to characterize the performance of intact boars, crossbred progenies of 136 Pietrain boars mated to crossbred sows from three different breeding companies were tested on four test stations. A total of 598 boars were performance tested according to the rules of stationary performance testing in Germany. Beside common fattening and carcass composition traits, the concentrations of the boar taint components and testicular size parameters were recorded. All boars were genotyped with the PorcineSNP60 Illumina BeadChip. The GWAS were performed using the whole data set as well as in sub groups according to the line of origin. Besides an univariate GWAS approach, principal component (PC) techniques were applied to identify common expression pattern affecting the biosynthesis and the metabolism of androstenone.

Results

In total, 33 SNPs were significantly associated with at least one of the boar taint components. Only one SNP was identified being significant in both subgroups. The analyses of the testes size parameters revealed 31 significant associations. The numbers of significant SNPs within the genetic groups evidenced the strong population specific effects. A multivariate approach using PC revealed 33 significant associations for five different PC.

Conclusions

Based on Pietrain sired cross bred boars, the mayor objective of our study was to identify QTL for boar taint components and to detect pleiotropy among boar taint and testes traits. The high number of identified QTL revealed that boar taint traits are influenced by a large number of loci. Analyzing pleiotropy allowed identifying a QTL affecting androstenone and the gonasomatic index. In this region, QTL for ovulation rate and age at puberty of sows have been described in literature. This supports the physiological findings that the androstenone level of boars and reproduction performance of sows might be linked by an antagonistic relationship.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0194-z) contains supplementary material, which is available to authorized users.

Mapping colitis susceptibility in mouse models: distal chromosome 3 contains major loci related to Cdcs1

Inflammatory bowel disease (IBD) summarizes a group of chronic intestinal disorders with Crohn's disease and ulcerative colitis being most prominent. Though much effort is put into identification of causative factors, its etiology is still not understood. Risk factors for disease development include genetic predisposition and environmental triggers. Crucial for identification and analysis of relevant factors are mouse models. Experimental IBD in mice occurs spontaneously or is induced by chemicals, cell transfer, pathogens, or genetic mutation. These models were utilized for analyzing genetic contribution to disease and genotype-environmental interactions. In these studies, a variety of modifier loci were identified, thereby demonstrating the complexity of disease. A major contribution of distal chromosome 3 was independently replicated in several studies. The first colitogenic QTL in this region was detected using the IL-10-deficient mouse model and called cytokine deficiency-induced colitis susceptibility (Cdcs)1. This quantitative trait locus contains at least three subintervals with independent genetic factors. This locus or defined subintervals were replicated in at least seven studies, using models based on dysregulation of innate or adaptive immunity or pathogen control. In this review we illustrate the various models used for genetic mapping of susceptibility to experimental IBD and display Cdcs1-related loci as well as the mechanism of their contribution identified so far.

Strain-specific colitis susceptibility in IL10-deficient mice depends on complex gut microbiota-host interactions

BACKGROUND

Colitis susceptibility in Il10(-/-) mice depends on genetic background and microbiota composition. A major genetic locus mediating colitis susceptibility, Cdcs1, was transferred from susceptible C3Bir-Il10(-/-) to resistant B6-Il10(-/-) mice, resulting in susceptible congenic BC-R3-Il10(-/-) mice. The aim of this study was to determine the impact of microbiota on this differential colitis susceptibility using a Helicobacter hepaticus infection model.

METHODS

Parental C3Bir-Il10(-/-) , B6-Il10(-/-) , and congenic BC-R3-Il10(-/-) mice were inoculated with H. hepaticus and analyzed for inflammation. In parental Il10(-/-) mice, microbiota composition was determined by terminal restriction fragment length polymorphism (T-RFLP) and quantitative polymerase chain reaction (qPCR).

RESULTS

Most severe inflammation was observed in C3Bir-Il10(-/-) in the cecum, in BC-R3-Il10(-/-) in cecum and colon, and, unexpectedly, in B6-Il10(-/-) in the colon. C3Bir-Il10(-/-) and BC-R3-Il10(-/-) secreted significantly more interferon-gamma (IFNγ) and interleukin (IL)17 than B6-Il10(-/-) . T-RFLP analyses in C3Bir-Il10(-/-) and B6-Il10(-/-) mice revealed 1) a significant impact of H. hepaticus infection on species richness and diversity, and 2) strain differences in microbiota composition only after H. hepaticus infection. qPCR revealed higher numbers of Clostridia leptum and Bacteroides spp. in the cecum of infected C3Bir-Il10(-/-) mice, and Lactobacillus spp. in B6-Il10(-/-) mice.

CONCLUSIONS

Cdcs1 modifies the response to H. hepaticus infection. However, this infection alone does not reflect the original response to a complex colitogenic biota. H. hepaticus-induced inflammation altered intestinal microbiota in a mouse strain-specific manner. Bacteroides spp. became more abundant in susceptible C3Bir-Il10(-/-) , lactobacilli in B6-Il10(-/-) mice. Therefore, both host immune response and differential compositional changes of microbiota play a role in strain-specific colitis susceptibility in Il10(-/-) mice.

Recent insights into microbial triggers of interleukin-10 production in the host and the impact on infectious disease pathogenesis

Since its initial description as a Th2-cytokine antagonistic to interferon-alpha and granulocyte-macrophage colony-stimulating factor, many studies have shown various anti-inflammatory actions of interleukin-10 (IL-10), and its role in infection as a key regulator of innate immunity. Studies have shown that IL-10 induced in response to microorganisms and their products plays a central role in shaping pathogenesis. IL-10 appears to function as both sword and shield in the response to varied groups of microorganisms in its capacity to mediate protective immunity against some organisms but increase susceptibility to other infections. The nature of IL-10 as a pleiotropic modulator of host responses to microorganisms is explained, in part, by its potent and varied effects on different immune effector cells which influence antimicrobial activity. A new understanding of how microorganisms trigger IL-10 responses is emerging, along with recent discoveries of how IL-10 produced during disease might be harnessed for better protective or therapeutic strategies. In this review, we summarize studies from the past 5 years that have reported the induction of IL-10 by different classes of pathogenic microorganisms, including protozoa, nematodes, fungi, viruses and bacteria and discuss the impact of this induction on the persistence and/or clearance of microorganisms in the host.

Systems genetics of susceptibility to obesity-induced diabetes in mice

Inbred strains of mice are strikingly different in susceptibility to obesity-driven diabetes. For instance, deficiency in leptin receptor (db/db) leads to hyperphagia and obesity in both C57BL/6 and DBA/2 mice, but only on the DBA/2 background do the mice develop beta-cell loss leading to severe diabetes, while C57BL/6 mice are relatively resistant. To further investigate the genetic factors predisposing to diabetes, we have studied leptin receptor-deficient offspring of an F2 cross between C57BL/6J (db/+) males and DBA/2J females. The results show that the genetics of diabetes susceptibility are enormously complex and a number of quantitative trait loci (QTL) contributing to diabetes-related traits were identified, notably on chromosomes 4, 6, 7, 9, 10, 11, 12, and 19. The Chr. 4 locus is likely due to a disruption of the Zfp69 gene in C57BL/6J mice. To identify candidate genes and to model coexpression networks, we performed global expression array analysis in livers of the F2 mice. Expression QTL (eQTL) were identified and used to prioritize candidate genes at clinical trait QTL. In several cases, clusters of eQTLs colocalized with clinical trait QTLs, suggesting a common genetic basis. We constructed coexpression networks for both 5 and 12 wk old mice and identified several modules significantly associated with clinical traits. One module in 12 wk old mice was associated with several measures of hepatic fat content as well as with other lipid- and diabetes-related traits. These results add to the understanding of the complex genetic interactions contributing to obesity-induced diabetes.

Quantitative trait loci in a bacterially induced model of inflammatory bowel disease

Inflammatory bowel diseases (IBDs) are complex disorders caused by a combination of environmental, microbial, and genetic factors. Genome-wide association studies in humans have successfully identified multiple genes and loci associated with disease susceptibility, but the mechanisms by which these loci interact with each other and/or with environmental factors (i.e., intestinal microbiota) to cause disease are poorly understood. Helicobacter hepaticus-induced intestinal inflammation in mice is an ideal model system for elucidating the genetic basis of IBD susceptibility in a bacterially induced system, as there are significant differences in H. hepaticus-induced disease susceptibility among inbred mouse strains. Infected A/J mice develop acute overexpression of proinflammatory cytokines followed 2-3 months later by chronic cecal inflammation, whereas infected C57BL/6 mice fail to develop cecal inflammation or increased cytokine expression. The goal of this project was to use quantitative trait locus (QTL) mapping to evaluate genetic factors that contribute to the differential disease susceptibility between these two mouse strains. Using acute cecal IL-12/23p40 expression as a biomarker for disease susceptibility, QTL analysis of H. hepaticus-infected F(2) mice revealed involvement of multiple loci. The loci with the strongest association were located on Chromosome 3 and Chromosome 17, with logarithm of odds (LOD) scores of 6.89 and 3.09, respectively. Cecal expression of IL-12/23p40 in H. hepaticus-infected C57BL/6J-Chr3(A/J)/NaJ chromosome substitution mice had an intermediate phenotype, significantly higher than in resistant C57BL/6 but lower than in susceptible A/J mice, confirming the importance of this locus to the immune response to H. hepaticus infection.

Severity of innate immune-mediated colitis is controlled by the cytokine deficiency-induced colitis susceptibility-1 (Cdcs1) locus

Genetic modifier loci influence the phenotypic expression of many Mendelian traits; insight into disease pathogenesis gained from their identification in animal disease models may impact the treatment of human multigenic disorders. We previously described an innate immune-driven model of spontaneous ulcerative colitis in T-bet(-/-).Rag2(-/-) double-deficient mice that resembles human ulcerative colitis. On a BALB/c background, this disease is highly penetrant and results in the development of colorectal cancer. However, we observed that colitis in T-bet(-/-).Rag2(-/-) mice on a C57BL/6 background was significantly less severe. Quantitative trait locus analysis using an N2 backcross strategy revealed a single major quantitative trait locus on chromosome 3 that mapped to the Cdcs1 (cytokine deficiency-induced colitis susceptibility-1) locus previously identified in the Il10(-/-) and Gnai2(-/-) colitis models. Congenic introduction of the susceptible Cdcs1 interval from C3H/He into the C57BL/6 background restored colitis severity. Bone marrow reconstitution experiments further mapped the effect of host genetics on disease severity to the hematopoietic compartment. There were distinct differences in the expression of several Cdcs1 genes in bone marrow-derived dendritic cells from Cdcs1 congenic mice. We conclude that the Cdcs1 locus controls colitis severity in T-bet(-/-).Rag2(-/-) mice through innate immune cells.

A model selection approach for expression quantitative trait loci (eQTL) mapping

Identifying the genetic basis of complex traits remains an important and challenging problem with the potential to affect a broad range of biological endeavors. A number of statistical methods are available for mapping quantitative trait loci (QTL), but their application to high-throughput phenotypes has been limited as most require user input and interaction. Recently, methods have been developed specifically for expression QTL (eQTL) mapping, but they too are limited in that they do not allow for interactions and QTL of moderate effect. We here propose an automated model-selection-based approach that identifies multiple eQTL in experimental populations, allowing for eQTL of moderate effect and interactions. Output can be used to identify groups of transcripts that are likely coregulated, as demonstrated in a study of diabetes in mouse.

Bayesian mixture structural equation modelling in multiple-trait QTL mapping

Quantitative trait loci (QTLs) mapping often results in data on a number of traits that have well-established causal relationships. Many multi-trait QTL mapping methods that account for correlation among the multiple traits have been developed to improve the statistical power and the precision of QTL parameter estimation. However, none of these methods are capable of incorporating the causal structure among the traits. Consequently, genetic functions of the QTL may not be fully understood. In this paper, we developed a Bayesian multiple QTL mapping method for causally related traits using a mixture structural equation model (SEM), which allows researchers to decompose QTL effects into direct, indirect and total effects. Parameters are estimated based on their marginal posterior distribution. The posterior distributions of parameters are estimated using Markov Chain Monte Carlo methods such as the Gibbs sampler and the Metropolis-Hasting algorithm. The number of QTLs affecting traits is determined by the Bayes factor. The performance of the proposed method is evaluated by simulation study and applied to data from a wheat experiment. Compared with single trait Bayesian analysis, our proposed method not only improved the statistical power of QTL detection, accuracy and precision of parameter estimates but also provided important insight into how genes regulate traits directly and indirectly by fitting a more biologically sensible model.

Serious limitations of the QTL/microarray approach for QTL gene discovery

BACKGROUND

It has been proposed that the use of gene expression microarrays in nonrecombinant parental or congenic strains can accelerate the process of isolating individual genes underlying quantitative trait loci (QTL). However, the effectiveness of this approach has not been assessed.

RESULTS

Thirty-seven studies that have implemented the QTL/microarray approach in rodents were reviewed. About 30% of studies showed enrichment for QTL candidates, mostly in comparisons between congenic and background strains. Three studies led to the identification of an underlying QTL gene. To complement the literature results, a microarray experiment was performed using three mouse congenic strains isolating the effects of at least 25 biometric QTL. Results show that genes in the congenic donor regions were preferentially selected. However, within donor regions, the distribution of differentially expressed genes was homogeneous once gene density was accounted for. Genes within identical-by-descent (IBD) regions were less likely to be differentially expressed in chromosome 2, but not in chromosomes 11 and 17. Furthermore, expression of QTL regulated in cis (cis eQTL) showed higher expression in the background genotype, which was partially explained by the presence of single nucleotide polymorphisms (SNP).

CONCLUSIONS

The literature shows limited successes from the QTL/microarray approach to identify QTL genes. Our own results from microarray profiling of three congenic strains revealed a strong tendency to select cis-eQTL over trans-eQTL. IBD regions had little effect on rate of differential expression, and we provide several reasons why IBD should not be used to discard eQTL candidates. In addition, mismatch probes produced false cis-eQTL that could not be completely removed with the current strains genotypes and low probe density microarrays. The reviewed studies did not account for lack of coverage from the platforms used and therefore removed genes that were not tested. Together, our results explain the tendency to report QTL candidates as differentially expressed and indicate that the utility of the QTL/microarray as currently implemented is limited. Alternatives are proposed that make use of microarray data from multiple experiments to overcome the outlined limitations.

Cdcs1 a major colitis susceptibility locus in mice; subcongenic analysis reveals genetic complexity

BACKGROUND

The cytokine-deficiency-induced colitis susceptibility (Cdcs)1 locus is a major modifier of murine inflammatory bowel disease (IBD) and was originally identified in experimental crosses of interleukin-10-deficient (Il10(-/-)) mice. Congenic mice, in which this locus was reciprocally transferred between IBD-susceptible C3H/HeJBir-Il10(-/-) and resistant C57BL/6J-Il10(-/-) mice, revealed that this locus likely acts by inducing innate hypo- and adaptive hyperresponsiveness, associated with impaired NF-kappaB responses of macrophages. The aim of the present study was to dissect the complexity of Cdcs1 by further development and characterization of reciprocal Cdcs1 congenic strains and to identify potential candidate genes in the congenic interval.

METHODS

In total, 15 reciprocal congenic strains were generated from Il10(-/-) mice of either C3H/HeJBir or C57BL/6J genetic backgrounds by 10 cycles of backcrossing. Colitis activity was monitored by histological grading. Candidate genes were identified by fine mapping of congenic intervals, sequencing, microarray analysis, and a high-throughput real-time reverse-transcription polymerase chain reaction (RT-PCR) approach using bone marrow-derived macrophages.

RESULTS

Within the originally identified Cdcs1-interval, 3 independent regions were detected that likely contain susceptibility-determining genetic factors (Cdcs1.1, Cdcs1.2, and Cdcs1.3). Combining results of candidate gene approaches revealed Fcgr1, Cnn3, Larp7, and Alpk1 as highly attractive candidate genes with polymorphisms in coding or regulatory regions and expression differences between susceptible and resistant mouse strains.

CONCLUSIONS

Subcongenic analysis of the major susceptibility locus Cdcs1 on mouse chromosome 3 revealed a complex genetic structure. Candidate gene approaches revealed attractive genes within the identified regions.

Analysis of Cd14 as a genetic modifier of experimental inflammatory bowel disease (IBD) in mice

BACKGROUND AND AIM

By combining QTL and gene expression analyses, we have previously identified Cd14 as a potential candidate gene contributing to the differential IBD susceptibility of C3H/HeJBir (C3/J)-Il10(-/-) mice [carrying IBD-resistance alleles at this QTL (Cdcs6)] and C57BL/6J (B6)-Il10(-/-) mice, corroborating studies that showed an association of a CD14-promoter polymorphism with Crohn's disease and ulcerative colitis. The aim of the present study was to analyze the molecular mechanisms leading to differential intestinal expression of Cd14 and its contribution to IBD development.

METHODS

Intestinal CD14 expression was assessed by FACS, immunohistochemistry, and ELISA on supernatants of primary epithelial cell and tissue cultures. RAW264.7 cells were stimulated with LPS and PGN in the presence or absence of CD14. Cd14 alleles were sequenced and promoters cloned for luciferase assays in transfected RAW264.7 cells. The severity of typhlocolitis between Cd14(-/-) and wild-type mice was compared in 2 distinct mouse models of IBD (acute DSS and Il10(-/-) ).

RESULTS

In the gut, CD14 was detected mainly in its soluble form (sCD14), with higher expression in C3/J-Il10(-/-) mice. Polymorphisms in C3/J mice caused higher activity of the Cd14 promoter (luciferase assays). Intestinal sCD14 concentrations influenced the LPS and PGN responses of RAW264.7 cells. In vivo, genetic deletion of Cd14 aggravated colitis in both mouse models of IBD.

CONCLUSIONS

Our study shows that Cd14-promoter polymorphisms affect CD14 expression and confirms the protective effect of CD14 against experimental IBD, potentially mediated by TLR2- and TLR4-dependent effects on intestinal barrier function. These findings support the concept that human CD14-promoter polymorphisms contribute to disease development.

Quantitative trait loci for resistance to Heligmosomoides bakeri and associated immunological and pathological traits in mice: comparison of loci on chromosomes 5, 8 and 11 in F2 and F6/7 inter-cross lines of mice

A comparison of F2 and F6/7 inter-cross lines of mice, derived from CBA and SWR parental strains, has provided strong evidence for several previously undetected quantitative trait loci (QTL) for resistance to Heligmosomoides bakeri. Five QTL affecting average faecal egg counts and/or worm burdens in week 6 were detected on mouse chromosomes 5 (Hbnr9 and Hbnr10), 8 (Hbnr11) and 11 (Hbnr13 and Hbnr14). Three QTL for faecal egg counts in weeks 4 and 6 were found on both chromosomes 5 (Hbnr9) and 11 (Hbnr13 and Hbnr14). Two QTL for the mucosal mast cell protease 1 (MCPT1) response were located on chromosomes 8 (Hbnr11) and 11 (Hbnr13), two for the IgG1 antibody response to adult worms on chromosomes 5 (Hbnr10) and 8 (Hbnr11), two for PCV in week 6 on chromosomes 5 (Hbnr9) and 11 (Hbnr13), and two for the granulomatous response on chromosome 8 (Hbnr12) and 11 (Hbnr15). Our data emphasize that the control of resistance to H. bakeri is multigenic, and regulated by genes within QTL regions that have a complex range of hierarchical relationships.

A data-capture tool for mouse pathology phenotyping

The Mouse Disease Information System is a free Microsoft Access database (http://research.jax.org/faculty/sundberg/index.html) designed by veterinary pathologists to aid veterinary pathologists in data acquisition, analysis, and coordination of tissue-sample archives. Linking the system to the Mouse Anatomy and Mouse Pathology Ontologies provides controlled vocabulary (and spelling) for organ, tissue, and diagnosis. Severity scores provide a quantitative assessment of all lesions to enable quantitative trait locus analysis for large-scale studies. Individual diagnoses can be verified for their definition by online linkage to Pathbase.net. Histologic images can be accessed from Pathbase by using the Mouse Pathology Ontology directly for comparison with slides being viewed at the time of data entry and providing the user with a reference and a "virtual second opinion."

Bayesian composite model space approach for mapping quantitative trait Loci in variance component model

In this article, we successfully apply the novel model selection method, Bayesian composite model space approach which has been used to map quantitative trait loci (QTL) for allelic substitution model, to map QTL for variance component model. The novel model selection approach has two advantages compared to the reversible jump Markov chain Monte Carlo method. Firstly, it mixes well due to the fixedness of the model dimension; secondly, it can map multiple QTL with higher power especially in genome-wide QTL mapping; finally, in the new method, it is also easy to incorporate our prior information about the variance components, which may bring precise estimate for variance components. A series of simulation experiments were conducted to demonstrate the general characters of the proposed method. The computer program is written in FORTRAN language, which is also built into a software "BayesMapQTL", and they also can be used for real data analysis and are available for request.

Guanylate-binding protein-1 is expressed at tight junctions of intestinal epithelial cells in response to interferon-gamma and regulates barrier function through effects on apoptosis

Guanylate-binding protein-1 (GBP-1) is an interferon inducible large GTPase involved in endothelial cell proliferation and invasion. In this report, expression and function of GBP-1 were investigated in vitro in intestinal epithelia after exposure to interferon-gamma and in human colonic mucosa from individuals with inflammatory bowel disease (IBD). Interestingly, in contrast to other epithelia, GBP-1 distributed to the plasma membrane in intestinal epithelial cells where it colocalized with the tight junction protein coxsackie- and adenovirus receptor. In addition, expression of GBP-1 was upregulated in colonic epithelia of individuals with IBD. Downregulation of GBP-1 by siRNA resulted in enhanced permeability that correlated with increased apoptosis. Indeed, inhibition of caspase activity prevented the inhibition of barrier formation induced by the loss of GBP-1. These data suggest that GBP-1 is a novel marker of intestinal mucosal inflammation that may protect against epithelial apoptosis induced by inflammatory cytokines and subsequent loss of barrier function.

Integrating mouse anatomy and pathology ontologies into a phenotyping database: tools for data capture and training

The Mouse Disease Information System (MoDIS) is a data capture system for pathology data from laboratory mice designed to support phenotyping studies. The system integrates the mouse anatomy (MA) and mouse pathology (MPATH) ontologies into a Microsoft Access database facilitating the coding of organ, tissue, and disease process to recognized semantic standards. Grading of disease severity provides scores for all lesions that can then be used for quantitative trait locus (QTL) analyses and haplotype association gene mapping. Direct linkage to the Pathbase online database provides reference definitions for disease terms and access to photomicrographic images of similar diagnoses in other mutant mice. MoDIS is an open source and freely available program (http://research.jax.org/faculty/sundberg/index.html). This provides a valuable tool for setting up a mouse pathology phenotyping program.

Bayesian quantitative trait loci mapping for multiple traits

Most quantitative trait loci (QTL) mapping experiments typically collect phenotypic data on multiple correlated complex traits. However, there is a lack of a comprehensive genomewide mapping strategy for correlated traits in the literature. We develop Bayesian multiple-QTL mapping methods for correlated continuous traits using two multivariate models: one that assumes the same genetic model for all traits, the traditional multivariate model, and the other known as the seemingly unrelated regression (SUR) model that allows different genetic models for different traits. We develop computationally efficient Markov chain Monte Carlo (MCMC) algorithms for performing joint analysis. We conduct extensive simulation studies to assess the performance of the proposed methods and to compare with the conventional single-trait model. Our methods have been implemented in the freely available package R/qtlbim (http://www.qtlbim.org), which greatly facilitates the general usage of the Bayesian methodology for unraveling the genetic architecture of complex traits.

Gene network inference via structural equation modeling in genetical genomics experiments

Our goal is gene network inference in genetical genomics or systems genetics experiments. For species where sequence information is available, we first perform expression quantitative trait locus (eQTL) mapping by jointly utilizing cis-, cis-trans-, and trans-regulation. After using local structural models to identify regulator-target pairs for each eQTL, we construct an encompassing directed network (EDN) by assembling all retained regulator-target relationships. The EDN has nodes corresponding to expressed genes and eQTL and directed edges from eQTL to cis-regulated target genes, from cis-regulated genes to cis-trans-regulated target genes, from trans-regulator genes to target genes, and from trans-eQTL to target genes. For network inference within the strongly constrained search space defined by the EDN, we propose structural equation modeling (SEM), because it can model cyclic networks and the EDN indeed contains feedback relationships. On the basis of a factorization of the likelihood and the constrained search space, our SEM algorithm infers networks involving several hundred genes and eQTL. Structure inference is based on a penalized likelihood ratio and an adaptation of Occam's window model selection. The SEM algorithm was evaluated using data simulated with nonlinear ordinary differential equations and known cyclic network topologies and was applied to a real yeast data set.

Sensitivity to Escherichia coli Nissle 1917 in mice is dependent on environment and genetic background

Escherichia coli Nissle 1917 (EcN) is a well-characterized probiotic bacterium. Although genomic comparisons of EcN with the uropathogenic E. coli strain CFT073 revealed high degrees of similarity, EcN is generally considered a non-pathogenic organism. However, as recent evidence suggests that EcN is capable of inducing inflammatory responses in host intestinal epithelial cells, we aimed to investigate potential pathogenic properties of EcN in an in vivo model using various germ-free (GF) mouse strains. With the exception of C3H/HeJZtm mice, which carry a defective toll-like receptor (TLR)4-allele, no lesions were obvious in mice of different strains orally inoculated with EcN for 1 week, although organ cultures (blood, lung, mesenteric lymph node, pancreas, spleen, liver and kidney) tested positive to various degrees. C3H/HeJZtm mice inoculated with EcN became clinically ill and the majority died or had to be euthanized. Organs of all gnotobiotic C3H/HeJZtm mice were positive for EcN by culture; major histological findings were moderate to severe pyogranulomatous serositis, typhlitis and pancreatitis. Histological findings were corroborated by highly elevated tumour necrosis factor (TNF) serum levels. Lesions were not detected in specified pathogen free maintained C3H/HeJZtm mice, GF C3H/HeJ mice lacking the interleukin-10 gene, or GF C3H/HeJZtm mice that were inoculated with E. coli K12 strain MG1655 as a control. In addition, mild histological lesions were detected in Ztm:NMRI mice 3 months after oral inoculation with EcN. This study shows that EcN is capable of displaying a virulent phenotype in GF C3H/HeJZtm mice. Whether this phenotype is linked to the bacterium's probiotic nature should be the focus of further studies.

Quantitative trait loci associated with blood pressure of metabolic syndrome in the progeny of NZO/HILtJxC3H/HeJ intercrosses

In a previous study in 15 inbred mouse strains, we found highest and lowest systolic blood pressures in NZO/HILtJ mice (metabolic syndrome) and C3H/HeJ mice (common lean strain), respectively. To identify the loci involved in hypertension in metabolic syndrome, we performed quantitative trait locus (QTL) analysis for blood pressure with direction of cross as a covariate in segregating F2 males derived from NZO/HILtJ and C3H/HeJ mice. We detected three suggestive main-effect QTLs affecting systolic and diastolic blood pressures (SBP and DBP). We analyzed the first principle component (PC1) generated from SBP and DBP to investigate blood pressure. In addition to all the suggestive QTLs (Chrs 1, 3, and 8) in SBP and DBP, one suggestive QTL on Chr 4 was found in PC1 in the main scan. Simultaneous search identified two significant epistatic locus pairs (Chrs 1 and 4, Chrs 4 and 8) for PC1. Multiple regression analysis revealed three blood pressure QTLs (Bpq10, 100 cM on Chr 1; Bpq11, 6 cM on Chr 4; Bpq12, 29 cM on Chr 8) accounting for 29.4% of blood pressure variance. These were epistatic interaction QTLs constructing a small network centered on Chr 4, suggesting the importance of genetic interaction for development of hypertension. The blood pressure QTLs on Chrs 1, 4, and 8 were detected repeatedly in multiple studies using common inbred nonobese mouse strains, implying substantial QTL independent of development of obesity and insulin resistance. These results enhance our understanding of complicated genetic factors of hypertension in metabolic diseases.

Locating multiple interacting quantitative trait Loci using rank-based model selection

In previous work, a modified version of the Bayesian information criterion (mBIC) was proposed to locate multiple interacting quantitative trait loci (QTL). Simulation studies and real data analysis demonstrate good properties of the mBIC in situations where the error distribution is approximately normal. However, as with other standard techniques of QTL mapping, the performance of the mBIC strongly deteriorates when the trait distribution is heavy tailed or when the data contain a significant proportion of outliers. In the present article, we propose a suitable robust version of the mBIC that is based on ranks. We investigate the properties of the resulting method on the basis of theoretical calculations, computer simulations, and a real data analysis. Our simulation results show that for the sample sizes typically used in QTL mapping, the methods based on ranks are almost as efficient as standard techniques when the data are normal and are much better when the data come from some heavy-tailed distribution or include a proportion of outliers.

Principal component analysis of quantitative trait loci for immune response to adenovirus in mice

Data on the duration of transgene expression in the liver, the presence of cytotoxic T lymphocytes (CTLs) against adenovirus, and serum cytokines from 18 strains of C57BL/6 x DBA/2 (B x D) recombinant inbred mice were analyzed. Our aim was to detect quantitative trait loci (QTLs) that may have causal relationship with the duration of adenovirus-mediated transgene expression in the liver. Information from beta-galactosidase (LacZ) expression; CTL production; and serum levels of gamma interferon, tumor necrosis factor-alpha, and interleukin-6 30 days after intravenous injection of liver LacZ were summarized by principal component analysis and analyzed using maximum likelihood interval mapping implemented in the QTL cartographer software. Two principal component (PC) scores explained 82.5% of the phenotypic variance in the original variables and identified QTLs not identified by analysis of individual traits. The distribution of original variables among PCs was such that variables in PC1 were predominantly cytokines with little CTL response whereas LacZ and CTL were the predominant contributors to PC2 with practically no contribution from cytokines. PC1 was significantly associated with two QTLs on chromosomes 7 and 9 located at 57.5 cM and 41.01 cM, respectively. Five QTLs were significantly associated with PC2 on chromosomes 12 (23.01 and 31.01 cM) and 15 (29.21, 36.01, and 56.31 cM). These results illustrate the use of principal component analysis in mapping QTLs using multiple correlated traits.

Structural model analysis of multiple quantitative traits

We introduce a method for the analysis of multilocus, multitrait genetic data that provides an intuitive and precise characterization of genetic architecture. We show that it is possible to infer the magnitude and direction of causal relationships among multiple correlated phenotypes and illustrate the technique using body composition and bone density data from mouse intercross populations. Using these techniques we are able to distinguish genetic loci that affect adiposity from those that affect overall body size and thus reveal a shortcoming of standardized measures such as body mass index that are widely used in obesity research. The identification of causal networks sheds light on the nature of genetic heterogeneity and pleiotropy in complex genetic systems.

Disease states are often associated with multiple, correlated traits that may result from shared genetic and nongenetic factors. Genetic analysis of multiple traits can reveal a network of effects in which each trait is influenced by more than one genetic locus (heterogeneity) and different traits share one or more loci in common (pleiotropy). Physiological interactions independent of genetic factors may also contribute to the observed correlations. Structural equation modeling is proposed as a statistical method to characterize the architecture of multiple trait genetic systems. Application of structural equation modeling to body size, adiposity, and bone geometry traits illustrates how the effects of a genetic locus can be decomposed along direct and indirect paths that may be mediated through interactions with other traits. Using this technique the authors identify adiposity loci that act independently of loci affecting overall body size.

Cd14,Gbp1, andPla2g2a: three major candidate genes for experimental IBD identified by combining QTL and microarray analyses

Induction of inflammatory bowel (IBD)-like disease in mice by a targeted mutation in the Il10 gene ( Il10−/−) is inbred strain dependent. C3H/HeJBir (C3) mice are colitis susceptible, whereas C57BL/6J (B6) mice are resistant. Genetic dissection of this susceptibility revealed 10 colitogenic quantitative trait loci (QTL). The aim of this study was to identify valuable candidate genes by a combination of QTL mapping and microarray analyses. Sixteen genes were differentially expressed between B6- and C3- Il10−/−mice and were located within the QTL intervals. Three major candidate genes ( Cd14, Gbp1, Pla2g2a) showed prominent expression differences between B6- and C3- Il10−/−as well as between B6 and C3 wild-type mice, which was confirmed by semiquantitative or real-time RT-PCR. Because strain differences are known for Gbp1 and Pla2g2a, further analyses focused on Cd14. Western blot analysis revealed strain differences also on the protein level. Cd14 expression in animals with defective and intact Toll-like receptor (TLR)4 signaling (C3, C3H/HeN, B6, B6- Tlr4tm1Aki) make the TLR4 defect of C3 mice unlikely to be the reason for higher Cd14 expression. Less Cd14 expression in germ-free mice indicates a contribution of the microflora on Cd14 expression. Stimulation of naive peritoneal macrophages with bacterial antigens showed lower CD14 surface expression in B6 than in C3 mice. In conclusion, the large number of candidate genes was reduced to three major candidates that play an important role in inflammatory processes and immune response. Strain differences for them are already known or are shown in this study.

A quantitative trait loci analysis to map genes involved in lipopolysaccharide-induced inflammatory response: identification of macrophage scavenger receptor 1 as a candidate gene

Septic shock, which is a major complication observed after trauma and other human diseases, is likely the product of a prolonged and poorly controlled systemic inflammatory response. Symptoms of sepsis can be partially reproduced by injection of bacterial LPS in mice. Differences in mortality between C57BL/6J(high) and A/J(low) mice after LPS injection have been previously observed and correlated with differences in the inflammatory response between these two inbred strains. In the present study, we have mapped four loci responsible for differences in levels of LPS-induced IL-10, named modifier of IL-10, between the two strains. A locus within mouse chromosome 8 was confirmed using chromosome 8 consomic mice. This locus was further reduced in size by haplotype analysis and evaluated by the presence of potential candidate genes. The macrophage scavenger receptor 1 (Msr1) within this locus emerged as a candidate gene based on differences at the expression and structural levels between C57BL/6J and A/J mice. In comparison with wild-type (C57BL/6J) mice, Msr1 knockout mice displayed reduced levels of LPS-induced IL-10, but not of TNF-alpha or IL-6, confirming a specific role for this gene in the regulation of IL-10. These results suggest that Msr1 is involved in the regulation of the anti-inflammatory process, thus offering a new perspective on the molecular mechanisms involved in endotoxemia and sepsis.

Environment as a Critical Factor for the Pathogenesis and Outcome of Gastrointestinal Disease: Experimental and Human Inflammatory Bowel Disease and Helicobacter-Induced Gastritis

Environmental factors play an important role in the manifestation, course, and prognosis of diseases of the gastrointestinal tract such as inflammatory bowel disease (IBD) and Helicobacter pylori-induced gastritis. These two disease complexes were chosen for a discussion of the contribution of environmental factors to the disease outcome in humans and animal models. Dissecting complex diseases like IBD and Helicobacter-induced gastritis has shown that the outcome of disease depends on the allelic constellation of a host and the microbial and physical environments. Host alleles predisposing to a disease in one genomic and/or environmental milieu may not be deleterious in other constellations; on the other hand, microbes can have different effects in different hosts and under different environmental conditions. The impact of the complex interaction between host genetics and environmental factors, particularly microflora, also underlines the importance of a defined genetic background and defined environments in animal studies and is indicative of the difficulties in analyzing complex diseases in humans.

Cdcs1, a major colitogenic locus in mice, regulates innate and adaptive immune response to enteric bacterial antigens

BACKGROUND & AIMS

The absence of interleukin 10, a key cytokine in gut homeostasis, causes severe colitis in C3H/HeJBir but not C57BL/6J mice. The major modifier for colitis was mapped on chromosome 3 and designated cytokine deficiency-induced colitis susceptibility 1 (Cdcs1). We developed reciprocal Cdcs1 congenic stocks on both interleukin 10-deficient backgrounds to identify the susceptibility gene and its function.

METHODS

C3H/HeJBir congenic for the C57BL/6J-derived Cdcs1 allele and reciprocal C57BL/6J congenic for the C3H/HeJBir allele were analyzed for colitis development. Parental strains were compared by electrophoretic mobility shift assay to assess the candidacy of nuclear factor-kappaB p50 in the Cdcs1 interval. Functional differences were observed in innate and adaptive immune responses of parental and congenic stocks after bacterial ligand exposure in vitro (cytokine release from bone marrow-derived macrophage and dendritic cells) and in vivo (serum cytokines and primed CD4+ T cell proliferation).

RESULTS

Cdcs1 was positioned within a minimum 7-megabase interval containing nuclear factor-kappaB p50. C3H/HeJBir colitis was significantly diminished by the C57BL/6J genome in this interval. Conversely, colitis in C57BL/6J was significantly exacerbated by the reciprocal C3H/HeJBir genome. C3H/HeJBir macrophages constitutively expressed higher nuclear factor-kappaB p50. Functional assays showed that C3H/HeJBir showed reduced innate responsiveness both in vivo and in vitro to bacterial ligands but showed increased CD4 T-cell responses compared with C57BL/6J. This differential responsiveness was controlled by the respective allele at Cdcs1.

CONCLUSIONS

The colitogenic Cdcs1 allele impairs innate immunity to bacterial products and in turn skews the adaptive immune response toward compensatory hyperresponsiveness and chronic intestinal inflammation.

Association of a lithogenic Abcg5/Abcg8 allele on Chromosome 17 (Lith9) with cholesterol gallstone formation in PERA/EiJ mice

To examine further the genetic determinants of cholesterol gallstone susceptibility in inbred mice, we performed quantitative trait locus (QTL) analysis of an intercross of gallstone-susceptible PERA/EiJ and gallstone-resistant DBA/2J inbred mice. Three hundred twenty-four F2 offspring were phenotyped for cholelithiasis during consumption of a lithogenic diet and genotyped using microsatellite markers. Linkage analysis was performed by interval mapping. In addition, we analyzed the combined datasets from this cross and from an independent cross of strain PERA and gallstone-resistant I/Ln mice. QTL mapping detected one significant new gallstone susceptibility (Lith) locus on Chromosome 13 (Lith15). A second significant QTL on Chr 6 (Lith16) confirmed a previous QTL. Furthermore, suggestive QTLs confirmed Lith loci from previous crosses on Chromosomes 1, 2, 5, 16 and X. QTL analysis of the dataset derived from the combined crosses increased the detection power and narrowed confidence intervals of Lith loci on Chromosomes 2, 6, 13, and 16. Moreover, the analysis of combined datasets revealed a shared QTL between both crosses on Chromosome 17 (Lith9). Significantly higher mRNA expression of Abcg5 and Abcg8 in strain PERA compared with strains I/Ln and DBA/2 further substantiated that the PERA allele of Abcg5/Abcg8 was responsible for lithogenicity underlying Lith9.

Enhanced egg-induced immunopathology correlates with high IFN-gamma in murine schistosomiasis: identification of two epistatic genetic intervals

The genetic basis of dissimilar immunopathology development among mouse strains infected with Schistosoma mansoni is not known. We performed a multipoint parametric linkage analysis on a cohort of F(2) mice, offspring of brother-sister mating between (high pathology CBA x low pathology BL/6)F(1) mice, to examine whether the observed differences in the type of immune response or the extent of hepatic immunopathology are linked to any particular genomic intervals. The F(2) mice exhibited cytokine responses and immunopathologies that revealed a statistically significant correlation between prominent egg Ag-stimulated IFN-gamma production by mesenteric lymph node cells and hepatic egg granuloma size. Increased IFN-gamma production showed suggestive linkage to a dominant CBA locus on chromosome 1 and a recessive CBA locus on chromosome 5; significantly, there was an epistatic interaction between the two IFN-gamma loci. An additional locus with suggestive linkage to granuloma formation and a CBA-recessive mode of inheritance was mapped to centromeric chromosome 13. Our analysis identified the first three genetic regions that appear to influence the immunopathology in murine schistosomiasis; however, further congenic dissection studies will furnish a more precise understanding of the genetic control of this disease.

Refined histopathologic scoring system improves power todetect colitis QTL in mice

Induction of colitis in mice by a targeted mutation in the I110 gene is inbred strain dependent. C3H/ HeJBir (C3H) mice are colitis susceptible while C57BL/6J (B6) mice are resistant. Identification of quantitative trait loci (QTL) determining the differential strain responsiveness requires histopathologic scoring of multiple lesion subphenotypes in both cecum and colon. Here we show that ability to detect a major C3H-derived QTL on Chr 3 (cytokine deficiency-induced colitis susceptibility 1, Cdcs1) was critically dependent upon the degree of refinement of the histopathologic scoring system. QTL mapping was performed using a first-back-cross population of interleukin-10-deficient mice and applying two different grading systems to assess lesion subphenotypes. The same histological specimens were scored by two independent pathologists using either a very detailed scoring system for four subphenotypes developed at The Jackson Laboratory (TJL) or a simpler scoring system developed at the Hannover Medical School (MHH). The more detailed TJL subphenotyping protocol increased power to identify Cdcs1 (a maximum LOD score of 4.28 versus a LOD score of 1.77 when using the abbreviated MHH subphenotyping scoring system). This study shows that for QTL mapping in a mouse model of colitis, in which histology represents the gold standard for phenotyping, ability to detect linkage is critically dependent upon the degree of refinement adopted for separately scoring the multiple histopathologic lesions comprising this complex phenotype.

Genetic analysis of macrophage characteristics as a tool to identify tumor susceptibility genes: mapping of three macrophage-associated risk inflammatory factors, marif1, marif2, and marif3

Genetic predisposition to cancer is influenced by allelic variation in tumor susceptibility genes (TSGs) as present in the germline. We previously demonstrated in the mouse that TSGs frequently participate in genetic interactions, indicating that they represent molecular networks. Inflammation may constitute one of the molecular networks underlying susceptibility to cancer by influencing the tumor microenvironment. Because macrophages play a key role in inflammation and are often associated with tumors, we argue that a subset of TSGs can be identified by examining the genetics of macrophage characteristics. A panel of inflammation-related assays was established to phenotype mouse bone marrow-derived macrophages, which included stimulation with lipopolysaccharides followed by measurement of secretion of tumor necrosis factor alpha and the p40 chain of interleukin-12 and of expression of inducible nitric oxide synthase and cyclooxygenase-2. This panel of assays was used for linkage analysis and applied to bone marrow-derived macrophages derived from individual mice of segregating crosses between inbred strain O20 and the highly related strains NTX-10 and NTX-20, which differed from O20 in only 10% of their genome, to reduce genetic complexity. Three macrophage-associated risk inflammatory factors were mapped-Marif1, Marif2, and Marif3-that each affected several inflammation-related assays, confirming that they function within molecular networks. Moreover, Marif1 and Marif2 were localized in regions with established linkage for both quantitative and qualitative aspects of lung cancer susceptibility. These studies provide a novel approach to investigate the genetics of microenvironmental influence on predisposition to tumorigenesis, thereby contributing to development of new strategies that aim to prevent or treat cancer.

Mapping major quantitative trait loci for postnatal growth in an intersubspecific backcross between C57BL/6J and Philippine wild mice by using principal component analysis

A number of quantitative trait loci (QTLs) for postnatal growth have previously been reported in mice. As effects of the QTLs are usually small and similar to one another in magnitude, it is generally difficult to know which loci are major contributors to postnatal growth. We applied principal component analysis to a genome-wide search for QTLs affecting postnatal growth in body weight weekly recorded from 3 to 10 weeks of age in an intersubspecific backcross population of C57BL/6J inbred mice (Mus musculus domesticus) and wild mice (M. m. castaneus) captured in the Philippines, in order to discover new QTLs from a gene pool of the wild mice and uncover major loci underlying variation in postnatal growth. Principal component analysis classified phenotypic variation in body weights at different ages into two independent principal components: the first principal component (PC1) extracted information on the entire growth process and the second principal component (PC2) contrasted middle (3-6 weeks of age) with late (6-10 weeks) growth phases. Simple interval mapping and composite interval mapping revealed 10 significant QTLs with main effects on PC1 or PC2 on eight chromosomes. Of these, the six main-effect QTLs interacted epistatically with one another or three new additional QTLs on different chromosomal regions without main effects. Several of the identified QTLs with main effects and/or epistatic interaction effects appeared to be sex specific. These results suggest that the identified 13 QTLs, most of which affected the entire growth process, are very important contributors to complex genetic networks of postnatal growth.

Dimension reduction for mapping mRNA abundance as quantitative traits

The advent of sophisticated genomic techniques for gene mapping and microarray analysis has provided opportunities to map mRNA abundance to quantitative trait loci (QTL) throughout the genome. Unfortunately, simple mapping of each individual mRNA trait on the scale of a typical microarray experiment is computationally intensive, subject to high sample variance, and therefore underpowered. However, this problem can be addressed by capitalizing on correlation among the large number of mRNA traits. We present a method to reduce the dimensionality for mapping gene expression data as quantitative traits. We used a blind method, principal components, and a sighted method, hierarchical clustering seeded by disease relevant traits, to define new traits composed of a small collection of promising mRNAs. We validated the principle of our approach by mapping the expression levels of metabolism genes in a population of F(2)-ob/ob mice derived from the BTBR and C57BL/6J strains. We found that lipogenic and gluconeogenic mRNAs, which are known targets of insulin action, were closely associated with the insulin trait. Multiple interval mapping and Bayesian interval mapping of this new trait revealed significant linkages to chromosome regions that were contained in loci associated with type 2 diabetes in this same mouse sample. As a further statistical refinement, we show that principal component analysis also effectively reduced dimensions for mapping phenotypes composed of mRNA abundances.

Interleukin-10-based therapy for inflammatory bowel disease

In recent years it has become clear that chronic inflammatory bowel disease (IBD), especially Crohn's disease (CD), is caused by a loss of tolerance against the autologous bacterial flora of the intestine. Tolerance against the indigenous flora requires optimal recognition of antigens by pattern recognition receptors and the presence of important regulatory cells and cytokines. Interleukin-10 (IL-10) has a major role in the regulatory network of cytokines controlling mucosal tolerance, and it is, therefore, not surprising that this cytokine is proposed as a potent anti-inflammatory biological therapy in chronic IBD. This review will discuss the characteristics of IL-10, its immunoregulatory properties in mice and humans, and the use of IL-10 as a treatment for CD. The review will summarise the clinical studies that have taken place and discuss the lessons learned from these trials. Finally, the advantages and disadvantages of promising new strategies of IL-10 treatment, including gene therapy and the use of genetically modified bacteria, will be discussed. Both novel therapies have been shown to be successful in animal models of disease, and clinical testing is currently underway. The future goal of IL-10 treatment should be focused on mucosal delivery and remission maintenance instead of remission induction. In conclusion, it can be said that despite the disappointing results of IL-10 therapy so far, there is still enough rationale for the use of IL-10 as an anti-inflammatory biological treatment in chronic IBD.

The immunological and genetic basis of inflammatory bowel disease

The inflammatory bowel diseases (IBDs), Crohn's disease and ulcerative colitis, are chronic inflammatory disorders of the gastrointestinal tract. Enormous progress has been made recently in understanding the pathogenesis of these diseases. Through the study of patients and mouse models, it has emerged that Crohn's disease is driven by the production of interleukin-12 (IL-12) and interferon-gamma (IFN-gamma), whereas ulcerative colitis is probably driven by the production of IL-13. A second area of progress is in the identification of specific genetic abnormalities that are responsible for disease. The most important finding is the identification of mutations in the gene that encodes NOD2 (nucleotide-binding oligomerization domain 2) protein in a subgroup of patients with Crohn's disease. Here, we discuss these recent findings and the implications for therapy.