A novel clinician interface to improve clinician access to up-to-date genetic results

OBJECTIVES

To understand the impact of GeneInsight Clinic (GIC), a web-based tool designed to manage genetic information and facilitate communication of test results and variant updates from the laboratory to the clinics, we measured the use of GIC and the time it took for new genetic knowledge to be available to clinicians.

METHODS

Usage data were collected across four study sites for the GIC launch and post-GIC implementation time periods. The primary outcome measures were the time (average number of days) between variant change approval and notification of clinic staff, and the time between notification and viewing the patient record.

RESULTS

Post-GIC, time between a variant change approval and provider notification was shorter than at launch (average days at launch 503.8, compared to 4.1 days post-GIC). After e-mail alerts were sent at launch, providers clicked into the patient record associated with 91% of these alerts. In the post period, clinic providers clicked into the patient record associated with 95% of the alerts, on average 12 days after the e-mail was sent.

DISCUSSION

We found that GIC greatly increased the likelihood that a provider would receive updated variant information as well as reduced the time associated with distributing that variant information, thus providing a more efficient process for incorporating new genetic knowledge into clinical care.

CONCLUSIONS

Our study results demonstrate that health information technology systems have the potential effectively to assist providers in utilizing genetic information in patient care.

Challenging question: can we diagnose Crohn's disease without histology?

No single test is diagnostic of Crohn's disease (CD). In the presence of a compatible clinical presentation, diagnosis is by convention confirmed by a combination of imaging, serologic, endoscopic and histologic investigations. This diagnostic recommendation should be maintained, even though histology is often 'compatible with' rather than 'diagnostic of' suspected CD. The importance of histology varies depending on the specific sites of macroscopic disease. Histology is particularly important in distinguishing type of inflammatory bowel disease, when the colon predominantly is involved, and in confirming CD when macroscopic disease is atypically located.

An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression

Functional characterization of causal variants present on risk haplotypes identified through genome-wide association studies (GWAS) is a primary objective of human genetics. In this report, we evaluate the function of a pair of tandem polymorphic dinucleotides, 42 kb downstream of the promoter of TNFAIP3, (rs148314165, rs200820567, collectively referred to as TT>A) recently nominated as causal variants responsible for genetic association of systemic lupus erythematosus (SLE) with tumor necrosis factor alpha inducible protein 3 (TNFAIP3). TNFAIP3 encodes the ubiquitin-editing enzyme, A20, a key negative regulator of NF-κB signaling. A20 expression is reduced in subjects carrying the TT>A risk alleles; however, the underlying functional mechanism by which this occurs is unclear. We used a combination of electrophoretic mobility shift assays (EMSA), mass spectrometry (MS), reporter assays, chromatin immunoprecipitation-PCR (ChIP-PCR) and chromosome conformation capture (3C) EBV transformed lymphoblastoid cell lines (LCL) from individuals carrying risk and non-risk TNFAIP3 haplotypes to characterize the effect of TT>A on A20 expression. Our results demonstrate that the TT>A variants reside in an enhancer element that binds NF-κB and SATB1 enabling physical interaction of the enhancer with the TNFAIP3 promoter through long-range DNA looping. Impaired binding of NF-κB to the TT>A risk alleles or knockdown of SATB1 expression by shRNA, inhibits the looping interaction resulting in reduced A20 expression. Together, these data reveal a novel mechanism of TNFAIP3 transcriptional regulation and establish the functional basis by which the TT>A risk variants attenuate A20 expression through inefficient delivery of NF-κB to the TNFAIP3 promoter. These results provide critical functional evidence supporting a direct causal role for TT>A in the genetic predisposition to SLE.

A key objective of human genetics is the identification and characterization of variants responsible for association with complex diseases. A pair of single nucleotide polymorphisms (rs148314165, rs200820567) 42 kb downstream from the promoter of TNFAIP3, have been proposed as the variants responsible for association with systemic lupus erythematosus based on comprehensive genetic and bioinformatic analyses. TNFAIP3 encodes for the ubiquitin-editing enzyme, A20, which plays a central role in maintaining immune system homeostasis through restriction of NF-κB signaling. Cells that carry this risk haplotype express low levels of TNFAIP3 compared to cells carrying the nonrisk haplotype. How the risk alleles of rs148314165 and rs200820567 might influence low TNFAIP3 expression is unknown. In this paper, we demonstrate that these variants reside in an enhancer element that binds NF-κB and SATB1 enabling the interaction of the enhancer with the TNFAIP3 promoter through long-range DNA looping. Impaired binding of NF-κB directly to the risk alleles or shRNA-mediated knockdown of SATB1 inhibits interaction of the enhancer with the TNFAIP3 promoter resulting in reduced A20 expression. These results clarify the functional mechanism by which rs148314165 and rs200820567 attenuate A20 expression and support a causal role for these variants in the predisposition to autoimmune disease.

The ubiquitin ligase parkin mediates resistance to intracellular pathogens

Ubiquitin-mediated targeting of intracellular bacteria to the autophagy pathway is a key innate defense mechanism against invading microbes, including the important human pathogen Mycobacterium tuberculosis. However, the ubiquitin ligases responsible for catalyzing ubiquitin chains that surround intracellular bacteria are poorly understood. PARKIN is a ubiquitin ligase with a well-established role in mitophagy, and mutations in the PARKIN gene (Park2) lead to increased susceptibility to Parkinson’s disease. Surprisingly, genetic polymorphisms in the Park2 regulatory region are also associated with increased susceptibility to intracellular bacterial pathogens in humans, including Mycobacterium leprae and Salmonella typhi, but the function of PARKIN in immunity remains unexplored. Here we show that PARKIN plays a role in ubiquitin-mediated autophagy of M. tuberculosis. Both PARKIN-deficient mice and flies are sensitive to various intracellular bacterial infections, suggesting PARKIN plays a conserved role in metazoan innate defense. Moreover, our work reveals an unexpected functional link between mitophagy and infectious disease.

Costimulatory genes: hotspots of conflict between host defense and autoimmunity

To understand the adaptations of costimulatory molecules through mammalian evolution, Forni et al. (Forni et al., 2013) studied evolutionary selection in key costimulatory genes. Their results, presented in this issue of Immunity, suggest that the risk of autoimmmunity is balanced against efficacy of the anti-pathogen immune response.

Rethinking mechanisms of autoimmune pathogenesis

Why exactly some individuals develop autoimmune disorders remains unclear. The broadly accepted paradigm is that genetic susceptibility results in some break in immunological tolerance, may enhance the availability of autoantigens, and may enhance inflammatory responses. Some environmental insults that occur on this background of susceptibility may then contribute to autoimmunity. In this review we discuss some aspects related to inhibitory signaling and rare genetic variants, as well as additional factors that might contribute to autoimmunity including the possible role of clonal somatic mutations, the role of epigenetic events and the contribution of the intestinal microbiome. Genetic susceptibility alleles generally contribute to the loss of immunological tolerance, the increased availability of autoantigens, or an increase in inflammation. Apart from common genetic variants, rare loss-of-function genetic variants may also contribute to the pathogenesis of autoimmunity. Studies of an inhibitory signaling pathway in B cells helped identify a negative regulatory enzyme called sialic acid acetyl esterase. The study of rare genetic variants of this enzyme provides an illustrative example showing the importance of detailed functional analyses of variant alleles and the need to exclude functionally normal common or rare genetic variants from analysis. It has also become clear that pathways that are functionally impacted by either common or rare defective variants can also be more significantly compromised by gene expression changes that may result from epigenetic alterations. Another important and evolving area that has been discussed relates to the role of the intestinal microbiome in influencing helper T cell polarization and the development of autoimmunity.

Milestones in understanding of the pathogenesis of immunmediated intestinal disorders. Development of their diagnosis and therapy

In the last decades our knowledge has been enormously broadened about the structure and function of the gut associated lymphoid system. It was recognized how intricate and finely tuned connection exists between the gut bacterial flora and the intestinal mucosa. This subtle balance ensures mucosal homeostasis, which has a key role in organ defence against pathogens. However, at the same time this system makes possible the development of oral tolerance toward the commensals and the food antigens. In case of any disturbances in this finely tuned process, immunmediated intestinal disorders may easily develop. The first part of this paper reviews the structure and function of the mucosal immune system, while the second part surveys the pathogenesis, diagnosis and therapy of coeliac disease, inflammatory bowel disease and cow’s milk allergy induced enteropathy. Orv. Hetil., 2013, 154, 1512–1523.

Crosstalk between the intestinal microbiota and the innate immune system in intestinal homeostasis and inflammatory bowel disease

: Inflammatory bowel diseases are a set of complex and chronic disorders that arise in genetically predisposed individuals due to a lack of tolerance to the gut microflora. Although the intestinal microbiota is required for the proper development of the host and the maintenance of intestinal homeostasis, its dysbiosis is associated with inflammatory bowel diseases pathogenesis. In this review, we focus the discussion on the crosstalk between the innate immune system and the microbiota. We examine new findings from genetic and functional studies investigating the critical role of the intestinal epithelial cell layer and the processes that maintain its integrity in health and disease. We further explore the mechanisms of the mucosal innate immune system including dendritic cells, macrophages, and innate-like lymphocytes in mediating immunological tolerance at the steady state or pathogenic inflammatory responses in inflammatory bowel diseases.

Linking vitamin d deficiency to inflammatory bowel disease

Inflammatory bowel disease is associated with industrialization, and its incidence has increased markedly over time. The prospect of reversing these trends motivates the search for the agent(s) involved. Modernity entails several physical and behavioral modifications that compromise both the photosynthesis of cholecalciferol in the skin and of its bioavailability. Although deficiency in this "vitamin" has therefore emerged as a leading candidate, and despite the publication of a randomized control trial that showed a trend toward statistically significant benefit in Crohn's disease, its causal agency has yet to be demonstrated by an adequately powered study. We discuss the strengths and weaknesses of the case being made by epidemiologists, geneticists, clinicians, and basic researchers, and consolidate their findings into a model that provides mechanistic plausibility to the claim. Specifically, converging data sets suggest that local activation of vitamin D coordinates the activity of the innate and adaptive arms of immunity, and of the intestinal epithelium, in a manner that promotes barrier integrity, facilitates the clearance of translocated flora, and diverts CD4 T cell development away from inflammatory phenotypes. Because smoking is an important risk-altering exposure, we also discuss its newly established melanizing effect and other emerging evidence linking tobacco use to immune function through vitamin D pathways.

Update on primary sclerosing cholangitis

Primary sclerosing cholangitis (PSC) remains one of the most challenging conditions of clinical hepatology. There has been a steady growth in research to overcome this fact and the present review aims at summarizing the most recently published literature. The main emphasis will be put on the link of recent pathogenetic insights to clinical characteristics and patient management. With regard to pathogenesis, there is no consensus yet as to whether immune mediated injury or factors related to bile acid physiology are the most important. It also remains to be clarified whether PSC is a mixed bag of various secondary etiologies yet to be defined, or a disease entity predominantly represented by sclerosing cholangitis in the context of inflammatory bowel disease. Most important, there is no available medical therapy with proven influence on clinical end points, and timing of liver transplantation and patient follow-up are challenging due to the unpredictable and high risk of cholangiocarcinoma.

Genetic risk factors for Clostridium difficile infection in ulcerative colitis

BACKGROUND

Patients with inflammatory bowel disease (IBD) are at higher risk for Clostridium difficile infection (CDI). Disruption of gut microbiome and interaction with the intestinal immune system are essential mechanisms for pathogenesis of both CDI and IBD. Whether genetic polymorphisms associated with susceptibility to IBD are also associated with risk of CDI is unknown.

AIMS

To use a well-characterised and genotyped cohort of patients with UC to (i) identify clinical risk factors for CDI; (ii) examine if any of the IBD genetic risk loci were associated with CDI; and (iii) to compare the performance of predictive models using clinical and genetic risk factors in determining risk of CDI.

METHODS

We used a prospective registry of patients from a tertiary referral hospital. Medical record review was performed to identify all ulcerative colitis (UC) patients within the registry with a history of CDI. All patients were genotyped on the Immunochip. We examined the association between the 163 risk loci for IBD and risk of CDI using a dominant genetic model. Model performance was examined using receiver operating characteristics curves.

RESULTS

The study included 319 patients of whom 29 developed CDI (9%). Female gender and pancolitis were associated with increased risk, while use of anti-TNF was protective against CDI. Six genetic polymorphisms including those at TNFRSF14 [Odds ratio (OR) 6.0, P-value 0.01] were associated with increased risk while 2 loci were inversely associated. On multivariate analysis, none of the clinical parameters retained significance after adjusting for genetics. Presence of at least one high-risk locus was associated with an increase in risk for CDI (20% vs. 1%) (P = 6 × 10⁻⁹). Compared to 11% for a clinical model, the genetic loci explained 28% of the variance in CDI risk and had a greater AUROC.

CONCLUSION

Host genetics may influence susceptibility to Clostridium difficile infection in patients with ulcerative colitis.

Interleukin-17 immunity in pediatric Crohn disease and ulcerative colitis

OBJECTIVE

The present understanding of inflammatory bowel disease pathogenesis mainly relies on studies of adult patients. Therefore, we studied the balance between T-effector and regulatory cells in pediatric inflammatory bowel disease.

METHODS

Quantitative polymerase chain reaction and immunohistochemistry served to quantify the expression of immunological markers in mucosal biopsies and flow cytometry analysis was used in peripheral blood mononuclear cells.

RESULTS

Colonic interleukin (IL)-17+, IL-22, and IL-6 mRNA upregulation and increase in the number of colonic IL-17 cells were demonstrated in both Crohn disease (CD) and ulcerative colitis (UC). Likewise, colonic forkhead box P3 (FOXP3+) mRNA expression and the number of colonic FOXP3 cells were increased both in CD and in UC and were accompanied in CD also with increased numbers of FOXP3+CD25 High CD4 cells in peripheral blood. Ileal relation of IL-17/CD4 cells was increased only in CD.

CONCLUSIONS

We showed activation of colonic IL-17/IL-22 axis and upregulation of FOXP3 to occur both in pediatric CD and in UC, indicating shared immunological characteristics. Upregulation of IL-17 was restricted to colon in UC, but existed in the ileum and in the colon in active CD.

Molecular diagnosis of infantile onset inflammatory bowel disease by exome sequencing

Pediatric-onset inflammatory bowel disease (IBD) is known to be associated with severe disease, poor response to therapy, and increased morbidity and mortality. We conducted exome sequencing of two brothers from a non-consanguineous relationship who presented before the age of one with severe infantile-onset IBD, failure to thrive, skin rash, and perirectal abscesses refractory to medical management. We examined the variants discovered in all known IBD-associated and primary immunodeficiency genes in both siblings. The siblings were identified to harbor compound heterozygous mutations in IL10RA (c.784C>T, p.Arg262Cys; c.349C>T, p.Arg117Cys). Upon molecular diagnosis, the proband underwent successful hematopoietic stem cell transplantation and demonstrated marked clinical improvement of all IBD-associated clinical symptoms. Exome sequencing can be an effective tool to aid in the molecular diagnosis of pediatric-onset IBD. We provide additional evidence of the safety and benefit of HSCT for patients with IBD due to mutations in the IL10RA gene.

Analysis of cytokines and chemokines produced by whole blood, peripheral mononuclear and polymorphonuclear cells

Cytokines are immunomodulating proteins involved in cellular communication. The levels of different cytokines reflect the immune capabilities of a person. In literature both whole blood and peripheral blood mononuclear cells (PBMCs) are used, which might lead to different results. The choice between these different sources is not always explained. The goal of our experiments is to determine the cytokine response of whole blood, PBMCs and polymorphonuclear cells (PMNs) after stimulation with lipopolysaccharide (LPS). We used a multiplex analysis to determine a difference in cytokine secretion patterns. In general, PBMCs demonstrated the highest cytokine production and PMNs have an overall low cytokine production. CCL11 and interleukin-23 (IL-23) (and IL-12p40) were exclusively expressed in whole blood. IL-20, VEGF and GM-CSF were expressed only by PBMCs. This difference in expression could be explained by the bioactive components in serum, presence and interaction with granulocytes or platelets in whole blood, the anticoagulant heparin in whole blood and others. The expression of cytokines by cells is dependent on the microenvironment. Different conditions lead to different results. We recommend a thorough examination of the conditions before performing experiments.

DNA methylation in inflammatory bowel disease and beyond

Inflammatory bowel disease (IBD) is a consequence of the complex, dysregulated interplay between genetic predisposition, environmental factors, and microbial composition in the intestine. Despite a great advancement in identifying host-susceptibility genes using genome-wide association studies (GWAS), the majority of IBD cases are still underrepresented. The immediate challenge in post-GWAS era is to identify other causative genetic factors of IBD. DNA methylation has received increasing attention for its mechanistical role in IBD pathogenesis. This stable, yet dynamic DNA modification, can directly affect gene expression that have important implications in IBD development. The alterations in DNA methylation associated with IBD are likely to outset as early as embryogenesis all the way until old-age. In this review, we will discuss the recent advancement in understanding how DNA methylation alterations can contribute to the development of IBD.

Estimation and partition of heritability in human populations using whole-genome analysis methods

Understanding genetic variation of complex traits in human populations has moved from the quantification of the resemblance between close relatives to the dissection of genetic variation into the contributions of individual genomic loci. However, major questions remain unanswered: How much phenotypic variation is genetic; how much of the genetic variation is additive and can be explained by fitting all genetic variants simultaneously in one model, and what is the joint distribution of effect size and allele frequency at causal variants? We review and compare three whole-genome analysis methods that use mixed linear models (MLMs) to estimate genetic variation. In all methods, genetic variation is estimated from the relationship between close or distant relatives on the basis of pedigree information and/or single nucleotide polymorphisms (SNPs). We discuss theory, estimation procedures, bias, and precision of each method and review recent advances in the dissection of genetic variation of complex traits in human populations. By using genome-wide data, it is now established that SNPs in total account for far more of the genetic variation than the statistically highly significant SNPs that have been detected in genome-wide association studies. All SNPs together, however, do not account for all of the genetic variance estimated by pedigree-based methods. We explain possible reasons for this remaining "missing heritability."

Next-generation sequencing in understanding complex neurological disease

Next-generation sequencing techniques have made vast quantities of data on human genomes and transcriptomes available to researchers. Huge progress has been made towards understanding the basis of many Mendelian neurological conditions, but progress has been considerably slower in complex neurological diseases (multiple sclerosis, migraine, Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and so on). The authors review current next-generation sequencing methodologies and present selected studies illustrating how these have been used to cast light on the genetic etiology of complex neurological diseases with specific focus on multiple sclerosis. The authors highlight particular pitfalls in next-generation sequencing experiments and speculate on both clinical and research applications of these sequencing platforms for complex neurological disorders in the future.

High fat diet accelerates pathogenesis of murine Crohn's disease-like ileitis independently of obesity

BACKGROUND

Obesity has been associated with a more severe disease course in inflammatory bowel disease (IBD) and epidemiological data identified dietary fats but not obesity as risk factors for the development of IBD. Crohn's disease is one of the two major IBD phenotypes and mostly affects the terminal ileum. Despite recent observations that high fat diets (HFD) impair intestinal barrier functions and drive pathobiont selection relevant for chronic inflammation in the colon, mechanisms of high fat diets in the pathogenesis of Crohn's disease are not known. The aim of this study was to characterize the effect of HFD on the development of chronic ileal inflammation in a murine model of Crohn's disease-like ileitis.

METHODS

TNF(ΔARE/WT) mice and wildtype C57BL/6 littermates were fed a HFD compared to control diet for different durations. Intestinal pathology and metabolic parameters (glucose tolerance, mesenteric tissue characteristics) were assessed. Intestinal barrier integrity was characterized at different levels including polyethylene glycol (PEG) translocation, endotoxin in portal vein plasma and cellular markers of barrier function. Inflammatory activation of epithelial cells as well as immune cell infiltration into ileal tissue were determined and related to luminal factors.

RESULTS

HFD aggravated ileal inflammation but did not induce significant overweight or typical metabolic disorders in TNF(ΔARE/WT). Expression of the tight junction protein Occludin was markedly reduced in the ileal epithelium of HFD mice independently of inflammation, and translocation of endotoxin was increased. Epithelial cells showed enhanced expression of inflammation-related activation markers, along with enhanced luminal factors-driven recruitment of dendritic cells and Th17-biased lymphocyte infiltration into the lamina propria.

CONCLUSIONS

HFD feeding, independently of obesity, accelerated disease onset of small intestinal inflammation in Crohn's disease-relevant mouse model through mechanisms that involve increased intestinal permeability and altered luminal factors, leading to enhanced dendritic cell recruitment and promoted Th17 immune responses.

Intestinal epithelial vitamin D receptor signaling inhibits experimental colitis

The inhibitory effects of vitamin D on colitis have been previously documented. Global vitamin D receptor (VDR) deletion exaggerates colitis, but the relative anticolitic contribution of epithelial and nonepithelial VDR signaling is unknown. Here, we showed that colonic epithelial VDR expression was substantially reduced in patients with Crohn's disease or ulcerative colitis. Moreover, targeted expression of human VDR (hVDR) in intestinal epithelial cells (IECs) protected mice from developing colitis. In experimental colitis models induced by 2,4,6-trinitrobenzenesulfonic acid, dextran sulfate sodium, or CD4(+)CD45RB(hi) T cell transfer, transgenic mice expressing hVDR in IECs were highly resistant to colitis, as manifested by marked reductions in clinical colitis scores, colonic histological damage, and colonic inflammation compared with WT mice. Reconstitution of Vdr-deficient IECs with the hVDR transgene completely rescued Vdr-null mice from severe colitis and death, even though the mice still maintained a hyperresponsive Vdr-deficient immune system. Mechanistically, VDR signaling attenuated PUMA induction in IECs by blocking NF-κB activation, leading to a reduction in IEC apoptosis. Together, these results demonstrate that gut epithelial VDR signaling inhibits colitis by protecting the mucosal epithelial barrier, and this anticolitic activity is independent of nonepithelial immune VDR actions.

Analysis of single nucleotide polymorphisms in the region of CLDN2-MORC4 in relation to inflammatory bowel disease

AIM: To investigate a possible genetic influence of claudin (CLDN)1, CLDN2 and CLDN4 in the etiology of inflammatory bowel disease.

METHODS: Allelic association between genetic regions of CLDN1, CLDN2 or CLDN4 and patients with inflammatory bowel disease, Crohn’s disease (CD) or ulcerative colitis were investigated using both a case-control study approach (one case randomly selected from each of 191 Swedish inflammatory bowel disease families and 333 controls) and a family-based study (463 non-Swedish European inflammatory bowel disease -families). A nonsynonymous coding single nucleotide polymorphism in MORC4, located on the same linkage block as CLDN2, was investigated for association, as were two novel CLDN2 single nucleotide polymorphism markers, identified by resequencing.

RESULTS: A single nucleotide polymorphism marker (rs12014762) located in the genetic region of CLDN2 was significantly associated to CD (case-control allelic OR = 1.98, 95%CI: 1.17-3.35, P = 0.007). MORC4 was present on the same linkage block as this CD marker. Using the case-control approach, a significant association (case control allelic OR = 1.61, 95%CI: 1.08-2.41, P = 0.018) was found between CD and a nonsynonymous coding single nucleotide polymorphism (rs6622126) in MORC4. The association between the CLDN2 marker and CD was not replicated in the family-based study. Ulcerative colitis was not associated to any of the single nucleotide polymorphism markers.

CONCLUSION: These findings suggest that a variant of the CLDN2-MORC4 region predisposes to CD in a Swedish population.

Inflammatory bowel disease: an expanding global health problem

This review provides a summary of the global epidemiology of inflammatory bowel diseases (IBD). It is now clear that IBD is increasing worldwide and has become a global emergence disease. IBD, which includes Crohn’s disease (CD) and ulcerative colitis (UC), has been considered a problem in industrial-urbanized societies and attributed largely to a Westernized lifestyle and other associated environmental factors. Its incidence and prevalence in developing countries is steadily rising and has been attributed to the rapid modernization and Westernization of the population. There is a need to reconcile the most appropriate treatment for these patient populations from the perspectives of both disease presentation and cost. In the West, biological agents are the fastest-growing segment of the prescription drug market. These agents cost thousands of dollars per patient per year. The healthcare systems, and certainly the patients, in developing countries will struggle to afford such expensive treatments. The need for biological therapy will inevitably increase dramatically, and the pharmaceutical industry, healthcare providers, patient advocate groups, governments and non-governmental organizations should come to a consensus on how to handle this problem. The evidence that IBD is now affecting a much younger population presents an additional concern. Meta-analyses conducted in patients acquiring IBD at a young age also reveals a trend for their increased risk of developing colorectal cancer (CRC), since the cumulative incidence rates of CRC in IBD-patients diagnosed in childhood are higher than those observed in adults. In addition, IBD-associated CRC has a worse prognosis than sporadic CRC, even when the stage at diagnosis is taken into account. This is consistent with additional evidence that IBD negatively impacts CRC survival. A continuing increase in IBD incidence worldwide associated with childhood-onset of IBD coupled with the diseases’ longevity and an increase in oncologic transformation suggest a rising disease burden, morbidity, and healthcare costs. IBD and its associated neoplastic transformation appear inevitable, which may significantly impact pediatric gastroenterology and adult CRC care. Due to an infrastructure gap in terms of access to care between developed vs. developing nations and the uneven representation of IBD across socioeconomic strata, a plan is needed in the developing world regarding how to address this emerging problem.

Atherosclerosis susceptibility Loci identified in an extremely atherosclerosis-resistant mouse strain

Background

C3H/HeJ (C3H) mice are extremely resistant to atherosclerosis, especially males. To understand the underlying genetic basis, we performed quantitative trait locus (QTL) analysis on a male F₂ (the second generation from an intercross between 2 inbred strains) cohort derived from an intercross between C3H and C57BL/6 (B6) apolipoprotein E–deficient (Apoe^−/−) mice.

Methods and Results

Two hundred forty‐six male F₂ mice were started on a Western diet at 8 weeks of age and kept on the diet for 5 weeks. Atherosclerotic lesions in the aortic root and fasting plasma lipid levels were measured. One hundred thirty‐four microsatellite markers across the entire genome were genotyped. Four significant QTLs on chromosomes (Chr) 2, 4, 9, and 15 and 4 suggestive loci on Chr1, Chr4, and Chr7 were identified for atherosclerotic lesions. Unexpectedly, the C3H allele was associated with increased lesion formation for 2 of the 4 significant QTLs. Six loci for high‐density lipoprotein (HDL), 6 for non‐HDL cholesterol, and 3 for triglycerides were also identified. The QTL for atherosclerosis on Chr9 replicated Ath29, originally mapped in a female F₂ cohort derived from B6 and C3H Apoe^−/− mice. This locus coincided with a QTL for HDL, and there was a moderate, but statistically significant, correlation between atherosclerotic lesion sizes and plasma HDL cholesterol levels in F₂ mice.

Conclusions

These data indicate that most atherosclerosis susceptibility loci are distinct from those for plasma lipids except for the Chr9 locus, which exerts effect through interactions with HDL.

Genetic insights into common pathways and complex relationships among immune-mediated diseases

Shared aetiopathogenic factors among immune-mediated diseases have long been suggested by their co-familiality and co-occurrence, and molecular support has been provided by analysis of human leukocyte antigen (HLA) haplotypes and genome-wide association studies. The interrelationships can now be better appreciated following the genotyping of large immune disease sample sets on a shared SNP array: the 'Immunochip'. Here, we systematically analyse loci shared among major immune-mediated diseases. This reveals that several diseases share multiple susceptibility loci, but there are many nuances. The most associated variant at a given locus frequently differs and, even when shared, the same allele often has opposite associations. Interestingly, risk alleles conferring the largest effect sizes are usually disease-specific. These factors help to explain why early evidence of extensive 'sharing' is not always reflected in epidemiological overlap.

Inflammatory bowel disease therapies and gut function in a colitis mouse model

Background. Exclusive enteral nutrition (EEN) is a well-established approach to the management of Crohn's disease. Aim. To determine effects of EEN upon inflammation and gut barrier function in a colitis mouse model. Methods. Interleukin-10-deficient mice (IL-10^−/−) were inoculated with Helicobacter trogontum and then treated with EEN, metronidazole, hydrocortisone, or EEN and metronidazole combination. Blood and tissue were collected at 2 and 4 weeks with histology, mucosal integrity, tight junction integrity, inflammation, and H. trogontum load evaluated. Results. H. trogontum induced colitis in IL-10^−/− mice with histological changes in the cecum and colon. Elevated mucosal IL-8 mRNA in infected mice was associated with intestinal barrier dysfunction indicated by decreased transepithelial electrical resistance and mRNA of tight junction proteins and increased short-circuit current, myosin light chain kinase mRNA, paracellular permeability, and tumor necrosis factor-α and myeloperoxidase plasma levels (P < 0.01 for all comparisons). EEN and metronidazole, but not hydrocortisone, treatments restored barrier function, maintained gut barrier integrity, and reversed inflammatory changes along with reduction of H. trogontum load (versus infected controls P < 0.05). Conclusion. H. trogontum infection in IL-10^−/− mice induced typhlocolitis with intestinal barrier dysfunction. EEN and metronidazole, but not hydrocortisone, modulate barrier dysfunction and reversal of inflammatory changes.

Type I IFNs regulate effector and regulatory T cell accumulation and anti-inflammatory cytokine production during T cell-mediated colitis

We explored the function of endogenous type I IFNs (IFN-1) in the colon using the T cell adoptive transfer model of colitis. Colon mononuclear phagocytes (MPs) constitutively produced IFN-1 in a Toll/IL-1R domain-containing adapter-inducing IFN-β-dependent manner. Transfer of CD4(+)CD45RB(hi) T cells from wild-type (WT) or IFN-α/β receptor subunit 1 knockout (IFNAR1(-/-)) mice into RAG(-/-) hosts resulted in similar onset and severity of colitis. In contrast, RAG(-/-) × IFNAR1(-/-) double knockout (DKO) mice developed accelerated severe colitis compared with RAG(-/-) hosts when transferred with WT CD4(+)CD45RB(hi) T cells. IFNAR signaling on host hematopoietic cells was required to delay colitis development. MPs isolated from the colon lamina propria of IFNAR1(-/-) mice produced less IL-10, IL-1R antagonist, and IL-27 compared with WT MPs. Accelerated colitis development in DKO mice was characterized by early T cell proliferation and accumulation of CD11b(+)CD103(-) dendritic cells in the mesenteric lymph nodes, both of which could be reversed by systemic administration of IL-1R antagonist (anakinra). Cotransfer of CD4(+)CD25(+) regulatory T cells (Tregs) from WT or IFNAR1(-/-) mice prevented disease caused by CD4(+)CD45RB(hi) T cells. However, WT CD4(+)CD25(+)Foxp3(GFP+) Tregs cotransferred with CD4(+)CD45RB(hi) T cells into DKO hosts failed to expand or maintain Foxp3 expression and gained effector functions in the colon. To our knowledge, these data are the first to demonstrate an essential role for IFN-1 in the production of anti-inflammatory cytokines by gut MPs and the indirect maintenance of intestinal T cell homeostasis by both limiting effector T cell expansion and promoting Treg stability.

Personalizing therapy for inflammatory bowel diseases

Inflammatory bowel diseases (IBDs; e.g., Crohn's disease [CD] and ulcerative colitis [UC]) are chronic immunologically mediated diseases characterized by frequent relapses, often requiring hospitalization and surgery. There is substantial heterogeneity in the progressive natural history of disease with cumulative accrual of bowel damage and impairment of functioning. Recent advances in therapeutics have significantly improved our ability to achieve disease remission; yet therapies remain expensive and are associated with significant side effects precluding widespread use in all patients with IBD. Consequently, algorithms for the management of patients with IBD require a personalized approach incorporating an individual's projected likely natural history, the probability of response to a specific therapeutic agent and an informed approach to management of loss of response to current therapies.

The increasing prevalence of inflammatory bowel diseases among Jewish adolescents and the sociodemographic factors associated with diagnosis

BACKGROUND

We investigated the prevalence and sociodemographic factors associated with diagnosis of inflammatory bowel diseases (IBD) among Jewish Israeli adolescents.

METHODS

A total of 953,684 Jewish Israeli adolescents (57.8% men) who underwent a general health examination at mean age 17.3 ± 0.5 years from 1998 to 2010 were included. A definite diagnosis of IBD was based on laboratory, endoscopy, and pathology reports. Covariate data included socioeconomic status (SES) as defined by the Israel Central Bureau Statistics, and origin and number of children in household.

RESULTS

A total of 2021 patients with IBD were identified (0.21%) in 13 annual cohorts. The prevalence of IBD increased from 149.4 cases per 100,000 to 301.0 cases per 100,000 in the first and last cohort (Ptrend = 0.003). Independent factors associated with occurrence of IBD were SES (high: odds ratio [OR] = 1.84, 95% confidence interval [CI]: 1.60-2.1, P < 0.001; medium: OR = 1.47, 95% CI: 1.3-1.69, P < 0.001; low: reference), Western origin (OR = 1.71, 95% CI: 1.53-1.90, P < 0.001; Asia Africa: reference), and male gender (OR = 1.21, 95% CI: 1.10-1.33, P < 0.001; female: reference). Four or more children in the household were associated with reduced OR for IBD [N ≥ 4: OR = 0.70, 95% CI: 0.62-0.72, P < 0.001, N = 1-3: reference]. The OR among adolescents of Western origin-high SES was 2.95 times higher compared with adolescents of Asia-African origin with low SES.

CONCLUSIONS

The prevalence of IBD doubled during the 13 years of the study period. Among this large cohort of Jewish adolescents, for each origin, higher SES was associated with increased occurrence of IBD.

How does genotype influence disease phenotype in inflammatory bowel disease?

Inflammatory bowel diseases (Crohn's disease and ulcerative colitis) are chronic immunologically mediated diseases of the gut. Advances in genetics have revolutionized our understanding of the pathogenesis of these conditions with 163 risk loci identified, encompassing a variety of immunologic functions. There is substantial heterogeneity in the natural history of these diseases with respect to disease onset, course, and progression to complications. There are also significant variations in response to therapies and susceptibility to therapy-related and disease-related complications. An important need in the field is to identify predictors of disease course, complications, and likelihood of response and adverse events to allow for targeted therapeutic decision making. The genotype of an individual in constant and non-modifiable, and thus could potentially fulfill the role of important predictors of these outcomes. In this review, we discuss the existing literature on the prediction of various disease phenotypes in Crohn's disease and ulcerative colitis using underlying genotype. We also identify gaps in the literature and suggest future directions for research. There is need for large, multi-institutional, and international collaborative consortia with efficient and detailed cohort accrual, phenotypic definition, genotyping, and dynamic assessments of external (e.g., diet) and internal (microbiome) environment to allow us to progress toward personalized and precision medicine in the management of these complex diseases.

Genes and functional GI disorders: from casual to causal relationship

BACKGROUND

The functional gastrointestinal disorders (FGID), and in particular irritable bowel syndrome (IBS), pose a considerable burden on health care and society, and negatively impact quality of life. These are common conditions of unknown etiology, and symptom-based criteria are currently the sole nosological tools for their clinical classification. Major insight into FGID pathophysiology is therefore needed and, in recent years, increasing hope has been put on genetic research for the identification of causative pathways. This is more advanced in IBS compared with other FGID, but it has still provided often indecipherable results and no unequivocal evidence of a pathogenetic role for any particular gene. Although thousands of genetic variants have been undoubtedly linked to human disease in hundreds of genome-wide association studies (GWAS), no similar effort has yet even been attempted in FGID. If meaningful, robust, and reproducible results are to be obtained for IBS and other FGID, we must shift gear and adopt these powerful hypothesis-free approaches through concerted actions and allocation of adequate resources. Provided these are in place, the major challenge will be, inevitably, the choice of the target phenotype(s) beyond a descriptive symptom-based classification.

PURPOSE

In view of these much awaited developments, salient results and difficulties inherent to IBS gene discovery are briefly summarized here.

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies

BACKGROUND & AIMS

Genome-wide association studies (GWAS) have identified 140 Crohn's disease (CD) susceptibility loci. For most loci, the variants that cause disease are not known and the genes affected by these variants have not been identified. We aimed to identify variants that cause CD through detailed sequencing, genetic association, expression, and functional studies.

METHODS

We sequenced whole exomes of 42 unrelated subjects with CD and 5 healthy subjects (controls) and then filtered single nucleotide variants by incorporating association results from meta-analyses of CD GWAS and in silico mutation effect prediction algorithms. We then genotyped 9348 subjects with CD, 2868 subjects with ulcerative colitis, and 14,567 control subjects and associated variants analyzed in functional studies using materials from subjects and controls and in vitro model systems.

RESULTS

We identified rare missense mutations in PR domain-containing 1 (PRDM1) and associated these with CD. These mutations increased proliferation of T cells and secretion of cytokines on activation and increased expression of the adhesion molecule L-selectin. A common CD risk allele, identified in GWAS, correlated with reduced expression of PRDM1 in ileal biopsy specimens and peripheral blood mononuclear cells (combined P = 1.6 × 10(-8)). We identified an association between CD and a common missense variant, Val248Ala, in nuclear domain 10 protein 52 (NDP52) (P = 4.83 × 10(-9)). We found that this variant impairs the regulatory functions of NDP52 to inhibit nuclear factor κB activation of genes that regulate inflammation and affect the stability of proteins in Toll-like receptor pathways.

CONCLUSIONS

We have extended the results of GWAS and provide evidence that variants in PRDM1 and NDP52 determine susceptibility to CD. PRDM1 maps adjacent to a CD interval identified in GWAS and encodes a transcription factor expressed by T and B cells. NDP52 is an adaptor protein that functions in selective autophagy of intracellular bacteria and signaling molecules, supporting the role of autophagy in the pathogenesis of CD.

Beyond gene discovery in inflammatory bowel disease: the emerging role of epigenetics

In the past decade, there have been fundamental advances in our understanding of genetic factors that contribute to the inflammatory bowel diseases (IBDs) Crohn's disease and ulcerative colitis. The latest international collaborative studies have brought the number of IBD susceptibility gene loci to 163. However, genetic factors account for only a portion of overall disease variance, indicating a need to better explore gene-environment interactions in the development of IBD. Epigenetic factors can mediate interactions between the environment and the genome; their study could provide new insight into the pathogenesis of IBD. We review recent progress in identification of genetic factors associated with IBD and discuss epigenetic mechanisms that could affect development and progression of IBD.

From genetics of inflammatory bowel disease towards mechanistic insights

Advancements in human genetics now poise the field to illuminate the pathophysiology of complex genetic disease. In particular, genome-wide association studies (GWAS) have generated insights into the mechanisms driving inflammatory bowel disease (IBD) and implicated genes shared by multiple autoimmune and autoinflammatory diseases. Thus, emerging evidence suggests a central role for the mucosal immune system in mediating immune homeostasis and highlights the complexity of genetic and environmental interactions that collectively modulate the risk of disease. Nevertheless, the challenge remains to determine how genetic variation can precipitate and sustain the inappropriate inflammatory response to commensals that is observed in IBD. Here, we highlight recent advancements in immunogenetics and provide a forward-looking view of the innovations that will deliver mechanistic insights from human genetics.

Functional profiling of the gut microbiome in disease-associated inflammation

The microbial residents of the human gut are a major factor in the development and lifelong maintenance of health. The gut microbiota differs to a large degree from person to person and has an important influence on health and disease due to its interaction with the human immune system. Its overall composition and microbial ecology have been implicated in many autoimmune diseases, and it represents a particularly important area for translational research as a new target for diagnostics and therapeutics in complex inflammatory conditions. Determining the biomolecular mechanisms by which altered microbial communities contribute to human disease will be an important outcome of current functional studies of the human microbiome. In this review, we discuss functional profiling of the human microbiome using metagenomic and metatranscriptomic approaches, focusing on the implications for inflammatory conditions such as inflammatory bowel disease and rheumatoid arthritis. Common themes in gut microbial ecology have emerged among these diverse diseases, but they have not yet been linked to targetable mechanisms such as microbial gene and genome composition, pathway and transcript activity, and metabolism. Combining these microbial activities with host gene, transcript and metabolic information will be necessary to understand how and why these complex interacting systems are altered in disease-associated inflammation.

Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits

For most complex traits, results from genome-wide association studies show that the proportion of the phenotypic variance attributable to the additive effects of individual SNPs, that is, the heritability explained by the SNPs, is substantially less than the estimate of heritability obtained by standard methods using correlations between relatives. This difference has been called the "missing heritability". One explanation is that heritability estimates from family (including twin) studies are biased upwards. Zuk et al. revisited overestimation of narrow sense heritability from twin studies as a result of confounding with non-additive genetic variance. They propose a limiting pathway (LP) model that generates significant epistatic variation and its simple parametrization provides a convenient way to explore implications of epistasis. They conclude that over-estimation of narrow sense heritability from family data ('phantom heritability') may explain an important proportion of missing heritability. We show that for highly heritable quantitative traits large phantom heritability estimates from twin studies are possible only if a large contribution of common environment is assumed. The LP model is underpinned by strong assumptions that are unlikely to hold, including that all contributing pathways have the same mean and variance and are uncorrelated. Here, we relax the assumptions that underlie the LP model to be more biologically plausible. Together with theoretical, empirical, and pragmatic arguments we conclude that in outbred populations the contribution of additive genetic variance is likely to be much more important than the contribution of non-additive variance.

Combining genetic mapping with genome-wide expression in experimental autoimmune encephalomyelitis highlights a gene network enriched for T cell functions and candidate genes regulating autoimmunity

The experimental autoimmune encephalomyelitis (EAE) is an autoimmune disease of the central nervous system commonly used to study multiple sclerosis (MS). We combined clinical EAE phenotypes with genome-wide expression profiling in spleens from 150 backcross rats between susceptible DA and resistant PVG rat strains during the chronic EAE phase. This enabled correlation of transcripts with genotypes, other transcripts and clinical EAE phenotypes and implicated potential genetic causes and pathways in EAE. We detected 2285 expression quantitative trait loci (eQTLs). Sixty out of 599 cis-eQTLs overlapped well-known EAE QTLs and constitute positional candidate genes, including Ifit1 (Eae7), Atg7 (Eae20-22), Klrc3 (eEae22) and Mfsd4 (Eae17). A trans-eQTL that overlaps Eae23a regulated a large number of small RNAs and implicates a master regulator of transcription. We defined several disease-correlated networks enriched for pathways involved in cell-mediated immunity. They include C-type lectins, G protein coupled receptors, mitogen-activated protein kinases, transmembrane proteins, suppressors of transcription (Jundp2 and Nr1d1) and STAT transcription factors (Stat4) involved in interferon signaling. The most significant network was enriched for T cell functions, similar to genetic findings in MS, and revealed both established and novel gene interactions. Transcripts in the network have been associated with T cell proliferation and differentiation, the TCR signaling and regulation of regulatory T cells. A number of network genes and their family members have been associated with MS and/or other autoimmune diseases. Combining disease and genome-wide expression phenotypes provides a link between disease risk genes and distinct molecular pathways that are dysregulated during chronic autoimmune inflammation.

Common genetic variants in the plasminogen activation pathway are not associated with multiple sclerosis

Matrix metalloproteinase 9 (MMP9) is involved in multiple sclerosis (MS) aetiology. Previously, we identified differential gene expression of plasminogen activation cascade genes in MS patients. Based on our gene expression results, we wanted to identify whether polymorphisms in the genes associated with the plasminogen pathway could predict MS risk. We genotyped 1153 trio families, 727 MS cases and 604 healthy controls for 17 polymorphisms in MMP9, plasminogen activator urokinase (PLAU), PLAU receptor (PLAUR) and serpin peptidase inhibitor/clade 2/member B2 (SERPINB2) genes. No associations were found between the 17 polymorphisms and MS. Also, gene expression levels were analysed according to genotype: no associations were observed. In conclusion despite the consistent evidence for the role of MMP9 and the plasminogen activation cascade in MS, we found no associations between genotype nor gene expression. This suggested there are other potentially modifiable factors influencing gene expression in MS.

miR-20b, miR-98, miR-125b-1*, and let-7e* as new potential diagnostic biomarkers in ulcerative colitis

AIM: To use microarray-based miRNA profiling of colonic mucosal biopsies from patients with ulcerative colitis (UC), Crohn’s disease (CD), and controls in order to identify new potential miRNA biomarkers in inflammatory bowel disease.

METHODS: Colonic mucosal pinch biopsies from the descending part were obtained endoscopically from patients with active UC or CD, quiescent UC or CD, as well as healthy controls. Total RNA was isolated and miRNA expression assessed using the miRNA microarray Geniom Biochip miRNA Homo sapiens (Febit GmbH, Heidelberg, Germany). Data analysis was carried out by principal component analysis and projection to latent structure-discriminant analysis using the SIMCA-P+12 software package (Umetrics, Umea, Sweden). The microarray data were subsequently validated by quantitative real-time polymerase chain reaction (qPCR) performed on colonic tissue samples from active UC patients (n = 20), patients with quiescent UC (n = 19), and healthy controls (n = 20). The qPCR results were analyzed with Mann-Whitney U test. In silico prediction analysis were performed to identify potential miRNA target genes and the predicted miRNA targets were then compared with all UC associated susceptibility genes reported in the literature.

RESULTS: The colonic mucosal miRNA transcriptome differs significantly between UC and controls, UC and CD, as well as between UC patients with mucosal inflammation and those without. However, no clear differences in the transcriptome of patients with CD and controls were found. The miRNAs with the strongest differential power were identified (miR-20b, miR-99a, miR-203, miR-26b, and miR-98) and found to be up-regulated more than a 10-fold in active UC as compared to quiescent UC, CD, and controls. Two miRNAs, miR-125b-1* and let-7e*, were up-regulated more than 5-fold in quiescent UC compared to active UC, CD, and controls. Four of the seven miRNAs (miR-20b, miR-98, miR-125b-1*, and let-7e*) were validated by qPCR and found to be specifically upregulated in patients with UC. Using in silico analysis we found several predicted pro-inflammatory target genes involved in various pathways, such as mitogen-activated protein kinase and cytokine signaling, which are both key signaling pathways in UC.

CONCLUSION: The present study provides the first evidence that miR-20b, miR-98, miR-125b-1*, and let-7e* are deregulated in patients with UC. The level of these miRNAs may serve as new potential biomarkers for this chronic disease.

Validating therapeutic targets through human genetics

More than 90% of the compounds that enter clinical trials fail to demonstrate sufficient safety and efficacy to gain regulatory approval. Most of this failure is due to the limited predictive value of preclinical models of disease, and our continued ignorance regarding the consequences of perturbing specific targets over long periods of time in humans. 'Experiments of nature' - naturally occurring mutations in humans that affect the activity of a particular protein target or targets - can be used to estimate the probable efficacy and toxicity of a drug targeting such proteins, as well as to establish causal rather than reactive relationships between targets and outcomes. Here, we describe the concept of dose-response curves derived from experiments of nature, with an emphasis on human genetics as a valuable tool to prioritize molecular targets in drug development. We discuss empirical examples of drug-gene pairs that support the role of human genetics in testing therapeutic hypotheses at the stage of target validation, provide objective criteria to prioritize genetic findings for future drug discovery efforts and highlight the limitations of a target validation approach that is anchored in human genetics.

Genetic variants associated with Crohn's disease

Crohn’s disease is an immune-related disorder characterized by inflammation of the gastrointestinal mucosa, which can occur in any area throughout the digestive tract. This life-long disease commonly presents with abdominal pain, diarrhea, vomiting, and weight loss. While the exact etiology of this disease is largely unknown, it is thought to arise from an interaction between microbial, immunological, and environmental factors in a genetically susceptible host, whereby the immune system attacks the intestine as it cross reacts against gut microbial antigens. The study of genetic variants associated with Crohn’s disease has shed light on our understanding of disease pathophysiology. A large number of genetic variants identified in Crohn’s disease are related to genes targeting microbial recognition and bacterial wall sensing, the most common being NOD2/CARD15 gene. This review will discuss the recent advance in our knowledge of genetic variants of this disease and how they influence the disease course and prognosis.

Irf8-regulated genomic responses drive pathological inflammation during cerebral malaria

Interferon Regulatory Factor 8 (IRF8) is required for development, maturation and expression of anti-microbial defenses of myeloid cells. BXH2 mice harbor a severely hypomorphic allele at Irf8 (Irf8^R294C) that causes susceptibility to infection with intracellular pathogens including Mycobacterium tuberculosis. We report that BXH2 are completely resistant to the development of cerebral malaria (ECM) following Plasmodium berghei ANKA infection. Comparative transcriptional profiling of brain RNA as well as chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) was used to identify IRF8-regulated genes whose expression is associated with pathological acute neuroinflammation. Genes increased by infection were strongly enriched for IRF8 binding sites, suggesting that IRF8 acts as a transcriptional activator in inflammatory programs. These lists were enriched for myeloid-specific pathways, including interferon responses, antigen presentation and Th1 polarizing cytokines. We show that inactivation of several of these downstream target genes (including the Irf8 transcription partner Irf1) confers protection against ECM. ECM-resistance in Irf8 and Irf1 mutants is associated with impaired myeloid and lymphoid cells function, including production of IL12p40 and IFNγ. We note strong overlap between genes bound and regulated by IRF8 during ECM and genes regulated in the lungs of M. tuberculosis infected mice. This IRF8-dependent network contains several genes recently identified as risk factors in acute and chronic human inflammatory conditions. We report a common core of IRF8-bound genes forming a critical inflammatory host-response network.

Cerebral malaria is a severe and often lethal complication from infection with Plasmodium falciparum which is driven in part by pathological host inflammatory response to parasitized red cells′ adherence in the brain microvasculature. However, the pathways that initiate and amplify this pathological neuroinflammation are not well understood. As susceptibility to cerebral malaria is variable and has been shown to be partially heritable, we have studied this from a genetic perspective using a mouse model of infection with P. berghei which induces experimental cerebral malaria (ECM). Here we show that mice bearing mutations in the myeloid transcription factor IRF8 and its heterodimerization partner IRF1 are completely resistant to ECM. We have identified the genes and associated networks that are activated by IRF8 during ECM. Loss-of-function mutations of several IRF8 targets are also shown to be protective. Parallel analysis of lungs infected with Mycobacterium tuberculosis show that IRF8-associated core pathways are also engaged during tuberculosis where they play a protective role. This contrast illustrates the balancing act required by the immune system to respond to pathogens and highlights a lynchpin role for IRF8 in both. Finally, several genes in these networks have been individually associated with chronic or acute inflammatory conditions in humans.

Why interleukin-10 supplementation does not work in Crohn’s disease patients

Inflammatory bowel diseases (IBD) such as Crohn’s disease (CD) or ulcerative colitis are chronic intestinal disorders, which are on the increase in “Westernised” countries. IBD can be caused by both genetic and environmental factors. Interleukin-10 (IL-10) is an immunoregulatory cytokine that has been identified as being involved in several diseases including IBD. Studies have shown that polymorphisms in the promoter region reduce serum levels of IL-10 and this reduction has been associated with some forms of IBD. Mouse models have shown promising results with IL-10 supplementation, as such IL-10 supplementation has been touted as being a possible alternative treatment for CD in humans. Clinical trials have shown that recombinant human IL-10 is safe and well tolerated up to a dose of 8 μg/kg. However, to date, the results of the clinical trials have been disappointing. Although CD activity was reduced as measured by the CD activity index, IL-10 supplementation did not result in significantly reduced remission rates or clinical improvements when compared to placebo. This review discusses why IL-10 supplementation is not effective in CD patients currently and what can be addressed to potentially make IL-10 supplementation a more viable treatment option in the future. Based on the current research we conclude that IL-10 supplementation is not a one size fits all treatment and if the correct population of patients is chosen then IL-10 supplementation could be of benefit.

A common 56-kilobase deletion in a primate-specific segmental duplication creates a novel butyrophilin-like protein

Background

The Butyrophilin-like (BTNL) proteins are likely to play an important role in inflammation and immune response. Like the B7 protein family, many human and murine BTNL members have been shown to control T lymphocytes response, and polymorphisms in human BTNL2 have been linked to several inflammatory diseases, such as pulmonary sarcoidosis, inflammatory bowel disease and neonatal lupus.

Results

In this study we provide a comprehensive population, genomic and transcriptomic analysis of a 56-kb deletion copy number variant (CNV), located within two segmental duplications of two genes belonging to the BTNL family, namely BTNL8 and BTNL3. We confirm the presence of a novel BTNL8*3 fusion-protein product, and show an influence of the deletion variant on the expression level of several genes involved in immune function, including BTNL9, another member of the same family. Moreover, by genotyping HapMap and human diversity panel (HGDP) samples, we demonstrate a clear difference in the stratification of the BTNL8_BTNL3-del allele frequency between major continental human populations.

Conclusion

Despite tremendous progress in the field of structural variation, rather few CNVs have been functionally characterized so far. Here, we show clear functional consequences of a new deletion CNV (BTNL8_BTNL3-del) with potentially important implication in the human immune system and in inflammatory and proliferative disorders. In addition, the marked population differences found of BTNL8_BTNL3-del frequencies suggest that this deletion CNV might have evolved under positive selection due to environmental conditions in some populations, with potential phenotypic consequences.

Mapping of immune-mediated disease genes

Genetic studies in immune-mediated diseases have yielded a large number of disease-associated loci. Here we review the progress being made in 12 such diseases, for which 199 independently associated non-HLA loci have been identified by genome-wide association studies since 2007. It is striking that many of the loci are not unique to a single disease but shared between different immune-mediated diseases. The challenge now is to understand how the unique and shared genetic factors can provide insight into the underlying disease biology. We annotated disease-associated variants using the Encyclopedia of DNA Elements (ENCODE) database and demonstrate that, of the predisposing disease variants, the majority have the potential to be regulatory. We also demonstrate that many of these variants affect the expression of nearby genes. Furthermore, we summarize results from the Immunochip, a custom array, which allows a detailed comparison between five of the diseases that have so far been analyzed using this platform.

Involvement of JAK/STAT signaling in the pathogenesis of inflammatory bowel disease

The Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway constitute the fulcrum in many vital cellular processes, including cell growth, differentiation, proliferation, and regulatory immune functions. Various cytokines, growth factors, and protein tyrosine kinases communicate through the JAK/STAT pathway and regulate the transcription of numerous genes. In addition to their critical roles in a plethora of key cellular activities, the JAK/STAT signaling pathways also have been implicated in the pathogenesis of several diseases, including inflammatory bowel disease (IBD), especially since a JAK inhibitor recently has been shown to be effective in the treatment of ulcerative colitis. The aim of this review is to highlight the recent findings on the regulatory mechanism of JAK/STAT signaling pathways and to reveal the evolving comprehension of their interface which might be of interest for clinicians involved in IBD therapy. Further, it is described how these signaling pathways have been exploited for the development of promising novel JAK inhibitors with anti-inflammatory effects verified in clinical trials.

Autophagy: a new target or an old strategy for the treatment of Crohn's disease?

In the past 5 years much progress has been made in understanding the molecular basis of Crohn's disease, a multifactorial chronic inflammatory disease of the gastrointestinal tract. Data suggest that hampered autophagy--the major lysosomal pathway for recycling of cytoplasmic material--might contribute to an increased susceptibility to Crohn's disease. Consequently, intense investigations have started to evaluate the potential value of autophagy as a therapeutic target and as a highly needed diagnostic tool. Interestingly, as well as the promising introduction of direct autophagic modulators, several drugs already used in the treatment of Crohn's disease might exert at least part of their effect through the regulation of autophagy. However, whether this phenomenon contributes to or rather counteracts their therapeutic use, remains to be determined and might prove to be highly compound-specific. Here we review the complex and emerging role of autophagy modulation in the battle against Crohn's disease. Moreover, we discuss the potential benefits and deleterious effects of autophagic regulation by both new and clinically used drugs.

Increasing incidence of paediatric inflammatory bowel disease in northern Stockholm County, 2002-2007

OBJECTIVES

A sharp increase in paediatric (younger than 16 years) inflammatory bowel disease (IBD) incidence was observed in northern Stockholm County, Sweden, in 1990-2001. The increasing incidence was primarily explained by a rising incidence of Crohn disease (CD). Here, we present an update on the trends in incidence of paediatric IBD, 2002-2007.

METHOD

Medical records of all children diagnosed as having suspected IBD in northern Stockholm County, 2002-2007, were scrutinised using defined diagnostic criteria. Disease extension, localisation, and behaviour at diagnosis were classified within the framework of the Paris classification.

RESULT

A total of 133 children were diagnosed as having IBD 2002-2007 corresponding to a sex- and age-standardised incidence (per 10 person-years) for paediatric IBD of 12.8 (95% CI 10.8-15.2). The standardised incidence was 9.2 (95% CI 7.5-11.2) for CD and 2.8 (95% CI 1.9-4.0) for ulcerative colitis (UC). A significant increasing incidence of UC (P < 0.05) was observed during the study period. No temporal trend was observed for the incidence of CD.

CONCLUSIONS

The incidence rate of paediatric IBD in northern Stockholm was significantly higher in 2002-2007 than that observed in our earlier study covering 1990-2001. The former sharp increase in incidence of paediatric CD seems, however, to have levelled out, although at a higher rate than reported from most other regions in the world. Although CD was still predominant, the observed increase in incidence of UC during the study period is notable.

Stem cell therapy in inflammatory bowel disease: which, when and how?

PURPOSE OF REVIEW

Stem cell therapy has emerged as a promising therapeutic strategy for inflammatory bowel diseases (IBDs). Currently, stem cell therapy is not part of the standard of care and is usually only performed as a part of clinical trials. In this review, clinical results, proposed underlying mechanisms, and future research directions will be discussed.

RECENT FINDINGS

Administration of mesenchymal stem cells (MSCs) and hematopoietic stem cells (HSCs) has been evaluated for IBD treatment over the past years. MSC therapy is being explored as a treatment option for fistulizing Crohn's disease and for luminal Crohn's disease. It is shown to be well tolerated, but results on efficacy are inconsistent. HSC transplantation seems to be very effective, but serious adverse events are common. Therefore, future research should focus on improving efficacy of MSC therapy, and on improvement of safety of HSC therapy.

SUMMARY

Both MSC and HSC therapy offer clinical potential, but currently are not routinely used for IBD treatment. MSC therapy seems well tolerated but results on efficacy are conflicting. HSC transplantation is shown to be effective but safety concerns remain. Nonetheless, for severe refractory IBD cases, stem cell therapy could well become the next-generation treatment option.