Gene-environment interactions in chronic inflammatory disease

Integrating omics: the future of IBD?

The complexity of IBD is well recognized as are the putative four major components of its pathogenesis, i.e. environment, genetic makeup, gut microbiota and mucosal immune response. Each of these components is extremely complex on its own, and at present should be more appropriately defined by the terms 'exposome', 'genome', 'microbiome' and 'immunome', respectively, based on the 'ome' suffix that refers to a totality of some sort. None of these 'omes' is apparently capable of causing IBD by itself; it is instead the intricate and reciprocal interaction among them, through the so-called 'IBD interactome', that results in the emergence of IBD, or more appropriately the 'IBD integrome'. To deal with and understand such overwhelming biological complexity, new approaches and tools are needed, and these are represented by 'omics', defined as the study of related sets of biological molecules in a comprehensive fashion, such as genomics, transcriptomics, proteomics, metabolomics, and so on. Numerous bioinformatics-based tools are available to explore and take advantage of the massive amount of information that can be generated by the analysis of the various omes and their interactions, aiming at identifying the molecular interactome underlying any particular status of health and disease. These novel approaches are fully applicable to IBD and allow us to achieve the ultimate goal of developing and applying personalized medicine and far more effective therapies to individual patients with Crohn's disease and ulcerative colitis. For the practicing gastroenterologist, an omics-based delivery of healthcare may be intimidating, but it must be accepted and implemented if he or she is to provide the best possible care to IBD patients.

Epigenomic regulation of host-microbiota interactions

The trillions of beneficial commensal microorganisms that normally reside in the gastrointestinal tract have emerged as a critical source of environmentally-derived stimuli that can impact health and disease. However, the underlying cellular and molecular mechanisms that recognize commensal bacteria-derived signals and regulate mammalian homeostasis are just beginning to be defined. Highly coordinated epigenomic modifications allow mammals to alter the transcriptional program of a cell in response to environmental cues. These modifications may play a key role in regulating the dynamic relationship between mammals and their microbiota. We review recent advances in understanding the interplay between the microbiota and mammalian epigenomic pathways, and highlight emerging findings that implicate a central role for histone deacetylases (HDACs) in orchestrating host-microbiota interactions.

Dissecting genetic architecture underlying seed traits in multiple environments

The seeds of flowering plants develop from double fertilization and play a vital role in reproduction and supplying human and animal food. The genetic variation of seed traits is influenced by multiple genetic systems, e.g., maternal, embryo, and/or endosperm genomes. Understanding the genetic architecture of seed traits is a major challenge because of this complex mechanism of multiple genetic systems, especially the epistasis within or between different genomes and their interactions with the environment. In this study, a statistical model was proposed for mapping QTL with epistasis and QTL-by-environment (QE) interactions underlying endosperm and embryo traits. Our model integrates the maternal and the offspring genomes into one mapping framework and can accurately analyze maternal additive and dominant effects, endosperm/embryo additive and dominant effects, and epistatic effects of two loci in the same or two different genomes, as well as interaction effects of each genetic component of QTL with environment. Intensive simulations under different sampling strategies, heritabilities, and model parameters were performed to investigate the statistical properties of the model. A set of real cottonseed data was analyzed to demonstrate our methods. A software package, QTLNetwork-Seed-1.0.exe, was developed for QTL analysis of seed traits.

Pharmacological investigation of a HPLC/MS standardized three herbal extracts containing formulae (Bu-Shen-Yi-Qi-Tang) on airway inflammation and hypothalamic-pituitary-adrenal axis activity in asthmatic mice

Bu-Shen-Yi-Qi-Tang (BSYQT) which is prescribed on the basis of clinical experience is commonly used in clinic of traditional Chinese medicine (TCM) for asthma treatment. The components of BSYQT include Radix Astragali (RA), Herba Epimedii (HE) and Radix Rehmanniae (RR). The aim of this study was to screen extracts of BSYQT with best anti-inflammatory activity in asthmatic mice, and separate and identify the chemical compounds in them. Our results suggested that 60% ethanol extract of herbs (H60) and granules (G60) of BSYQT were the two extracts with best anti-inflammatory activity and effects of H60 were a little better than that of G60. High-performance liquid chromatography coupled to electrospray ionization and quadrupole time-of-flight mass spectrometry (HPLC-ESI-Q-TOF-MS/MS) analysis of the major chemical compounds of H60 and G60 revealed that 56 and 42 peaks were identified separately in H60 and G60. Further analysis revealed that 38 compounds were identified shared by H60 and G60, and 18 compounds were only in H60. There were 25 compounds in HE, 6 compounds in RR and 7 compounds in RA in the 38 compounds shared by G60 and H60. These 38 chemical components were tentatively considered the material basis of the anti-inflammatory activity of G60 and H60. The differences in the amount of the 38 chemical components as well as the 18 chemical components only in H60 were tentatively considered responsible for the activity differences between H60 and G60. In conclusion, these results suggested that extracts of BSYQT had inhibitory effects on airway inflammation in asthmatic mice, and H60 and G60 demonstrated the best anti-inflammatory activity. The 38 chemical compounds shared by H60 and G60 were responsible for their anti-inflammatory activity in asthmatic mice, and the differences in chemical compounds contents and amounts between H60 and G60 were responsible for this activity differences. This work would provide support for further pharmacodynamic material basis study of BSYQT.

Elucidation of pathways driving asthma pathogenesis: development of a systems-level analytic strategy

Asthma is a genetically complex, chronic lung disease defined clinically as episodic airflow limitation and breathlessness that is at least partially reversible, either spontaneously or in response to therapy. Whereas asthma was rare in the late 1800s and early 1900s, the marked increase in its incidence and prevalence since the 1960s points to substantial gene × environment interactions occurring over a period of years, but these interactions are very poorly understood (1-6). It is widely believed that the majority of asthma begins during childhood and manifests first as intermittent wheeze. However, wheeze is also very common in infancy and only a subset of wheezy children progress to persistent asthma for reasons that are largely obscure. Here, we review the current literature regarding causal pathways leading to early asthma development and chronicity. Given the complex interactions of many risk factors over time eventually leading to apparently multiple asthma phenotypes, we suggest that deeply phenotyped cohort studies combined with sophisticated network models will be required to derive the next generation of biological and clinical insights in asthma pathogenesis.

Linking immunity, epigenetics, and cancer in inflammatory bowel disease

Most of what is known about the pathogenesis of inflammatory bowel disease (IBD) pertains to complex interplay between host genetics, immunity, and environmental factors. Epigenetic modifications play pivotal roles in intestinal immunity and mucosal homeostasis as well as mediating gene-environment interactions. In this article, we provide a historical account of epigenetic research either directly related or pertinent to the pathogenesis and management of IBD. We further collate emerging evidence supporting roles for epigenetic mechanisms in relevant aspects of IBD biology, including deregulated immunity, host-pathogen recognition and mucosal integrity. Finally, we highlight key epigenetic mechanisms that link chronic inflammation to specific IBD comorbidities, including colitis-associated cancer and discuss their potential utility as novel biomarkers or pharmacologic targets in IBD therapy.

[Prenatal sex-specific programming and chronic diseases or Finis Ab Orígine Pendet]

An increasing incidence of chronic immune diseases such as allergies, multiple sclerosis, and type 2 diabetes, as well as obesity and cardiovascular and psychiatric disorders has been reported over the last five decades. Since the human genome has not altered significantly over this period of time, gene-environment interactions are suspected to be responsible for these increased disease incidences. In this context, the prenatal period is believed to significantly contribute to altered disease susceptibilities, which could be associated with environmental factors to which pregnant women were exposed to. This observation has led to a concept entitled 'developmental origin of health and disease', a topic that is enjoying much attention in clinical and basic science research. The aim of these research endeavors is to postulate guidelines for primary disease prevention. Whilst the emerging insights from this field of research provide significant pieces of the puzzle, one area is still largely neglected: the clear identification of a sex-specific programming effect. Thus it is essential that such an approach becomes fully integrated in future research goals.

Immune mechanisms and development of childhood asthma

Early life influences are crucial for the development of distinct childhood asthma phenotypes, which are currently included under the term asthma syndrome. Improved characterisation of different childhood asthma phenotypes will help to elucidate specific underlying immune mechanisms--namely, endotypes. Besides genetics, epigenetics and environmental factors have an effect on innate and adaptive immune regulatory networks. Crucial determining factors for complex immune regulation and barrier function include family history of atopy, respiratory infections, microbiome, and nutrition. Recent diagnostic approaches, including biomarkers, might offer a unique opportunity to improve definitions of asthma sub-phenotypes, prediction of outcome, and treatment options, by referring to the underlying pathophysiology. For prevention and patient-individualised medicine, a multifactorial approach incorporating deep phenotyping and mathematical models for analysis to extend our present knowledge is needed.

Environmental changes, microbiota, and allergic diseases

During the last few decades, the prevalence of allergic disease has increased dramatically. The development of allergic diseases has been attributed to complex interactions between environmental factors and genetic factors. Of the many possible environmental factors, most research has focused on the most commonly encountered environmental factors, such as air pollution and environmental microbiota in combination with climate change. There is increasing evidence that such environmental factors play a critical role in the regulation of the immune response that is associated with allergic diseases, especially in genetically susceptible individuals. This review deals with not only these environmental factors and genetic factors but also their interactions in the development of allergic diseases. It will also emphasize the need for early interventions that can prevent the development of allergic diseases in susceptible populations and how these interventions can be identified.

Fetal exposure to maternal inflammation does not affect postnatal development of genetically-driven ileitis and colitis

Background: Chronic inflammatory disorders have been increasing in incidence over the past decades following geographical patterns of industrialization. Fetal exposure to maternal inflammation may alter organ functions and the offspring's disease risk. We studied the development of genetically-driven ileitis and colitis in response to maternal inflammation using mouse models.

Methods: Disease susceptible (Tnf^ΔARE/+ and IL10^−/−) and disease-free (Tnf^+/+ and IL10^−/+) offspring were raised in inflamed and non-inflamed dams. Ileal, caecal and colonic pathology was evaluated in the offspring at 8 or 12 weeks of age. Ly6G-positive cells in inflamed sections from the distal ileum and distal colon were analysed by immunofluorescence microscopy. Gene expression of pro-inflammatory cytokines was measured in whole tissue specimens by quantitative PCR. Microarray analyses were performed on laser microdissected intestinal epithelium. Caecal bacterial communities were assessed by Illumina sequencing of 16S rRNA amplicons.

Results: Disease severity, the number of infiltrated neutrophils as well as Tnf and Il12p40 mRNA expression were independent of maternal inflammation in the offspring of mouse models for ileitis (Tnf^ΔARE/+) and colitis (IL10^−/−). Although TNF-driven maternal inflammation regulated 2,174 (wild type) and 3,345 (Tnf^ΔARE/+) genes in the fetal epithelium, prenatal gene expression patterns were completely overwritten after birth. In addition, co-housing experiments revealed no change in phylogenetic diversity of the offspring's caecal microbiota in response to maternal inflammation. This is independent of the offspring's genotype before and after the onset of tissue pathology.

Conclusions: Disease risk and activity in mouse models of chronic ileitis and colitis was independent of the fetal exposure to maternal inflammation. Likewise, maternal inflammation did not alter the diversity and composition of offspring's caecal microbiota, clearly demonstrating that changes of the gene expression program in the fetal gut epithelium were not relevant for the development of chronic inflammatory disorders in the gut.

Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases

BACKGROUND

Common human diseases are caused by the complex interplay of genetic susceptibility as well as environmental factors. Due to the environment's influence on the epigenome, and therefore genome function, as well as conversely the genome's facilitative effect on the epigenome, analysis of this level of regulation may increase our knowledge of disease pathogenesis.

METHODS

In order to identify human-specific epigenetic influences, we have performed a novel genome-wide DNA methylation analysis comparing human, chimpanzee and rhesus macaque.

RESULTS

We have identified that the immunological Leukotriene B4 receptor (LTB4R, BLT1 receptor) is the most epigenetically divergent human gene in peripheral blood in comparison with other primates. This difference is due to the co-ordinated active state of human-specific hypomethylation in the promoter and human-specific increased gene body methylation. This gene is significant in innate immunity and the LTB4/LTB4R pathway is involved in the pathogenesis of the spectrum of human inflammatory diseases. This finding was confirmed by additional neutrophil-only DNA methylome and lymphoblastoid H3K4me3 chromatin comparative data. Additionally we show through functional analysis that this receptor has increased expression and a higher response to the LTB4 ligand in human versus rhesus macaque peripheral blood mononuclear cells. Genome-wide we also find human species-specific differentially methylated regions (human s-DMRs) are more prevalent in CpG island shores than within the islands themselves, and within the latter are associated with the CTCF motif.

CONCLUSIONS

This result further emphasises the exclusive nature of the human immunological system, its divergent adaptation even from very closely related primates, and the power of comparative epigenomics to identify and understand human uniqueness.

Microbial exposure and onset of allergic diseases - potential prevention strategies?

Chronic inflammatory diseases are a major health problem with global dimension. Particularly, the incidence of allergic diseases has been increased tremendously within the last decades. This world-wide trend clearly indicates the demand for new approaches in the investigation of early allergy development. Recent studies underlined the basic postulate of the hygiene hypothesis that early exposure to microbial stimuli plays a crucial role in the prevention of chronic inflammatory conditions in adulthood. There is ample evidence that, both, exogenous microbes and endogenous microbial communities, the human microbiota, shape the developing immune system and might be involved in prevention of pathologic pro-inflammatory trails. According to the Barker hypothesis, epidemiological studies pointed to transmaternal transmission from the mother to the offspring already in prenatal life. Experimental data from murine models support these findings. This state of the art review provides an overview on the current literature and presents new experimental concepts that point out to future application in the prevention of allergic diseases.

Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis

The development and severity of inflammatory bowel diseases and other chronic inflammatory conditions can be influenced by host genetic and environmental factors, including signals derived from commensal bacteria. However, the mechanisms that integrate these diverse cues remain undefined. Here we demonstrate that mice with an intestinal epithelial cell (IEC)-specific deletion of the epigenome-modifying enzyme histone deacetylase 3 (HDAC3(ΔIEC) mice) exhibited extensive dysregulation of IEC-intrinsic gene expression, including decreased basal expression of genes associated with antimicrobial defence. Critically, conventionally housed HDAC3(ΔIEC) mice demonstrated loss of Paneth cells, impaired IEC function and alterations in the composition of intestinal commensal bacteria. In addition, HDAC3(ΔIEC) mice showed significantly increased susceptibility to intestinal damage and inflammation, indicating that epithelial expression of HDAC3 has a central role in maintaining intestinal homeostasis. Re-derivation of HDAC3(ΔIEC) mice into germ-free conditions revealed that dysregulated IEC gene expression, Paneth cell homeostasis and intestinal barrier function were largely restored in the absence of commensal bacteria. Although the specific mechanisms through which IEC-intrinsic HDAC3 expression regulates these complex phenotypes remain to be determined, these data indicate that HDAC3 is a critical factor that integrates commensal-bacteria-derived signals to calibrate epithelial cell responses required to establish normal host-commensal relationships and maintain intestinal homeostasis.

Effect of barrier microbes on organ-based inflammation

The prevalence and incidence of chronic inflammatory disorders, including allergies and asthma, as well as inflammatory bowel disease, remain on the increase. Microbes are among the environmental factors that play an important role in shaping normal and pathologic immune responses. Several concepts have been put forward to explain the effect of microbes on the development of these conditions, including the hygiene hypothesis and the microbiota hypothesis. Recently, the dynamics of the development of (intestinal) microbial colonization, its effect on innate and adaptive immune responses (homeostasis), and the role of environmental factors, such as nutrition and others, have been extensively investigated. Furthermore, there is now increasing evidence that a qualitative and quantitative disturbance in colonization (dysbiosis) is associated with dysfunction of immune responses and development of various chronic inflammatory disorders. In this article the recent epidemiologic, clinical, and experimental evidence for this interaction is discussed.

Thymic stromal lymphopoietin-elicited basophil responses promote eosinophilic esophagitis

Eosinophilic esophagitis (EoE) is a food allergy-associated inflammatory disease characterized by esophageal eosinophilia. Current management strategies for EoE are nonspecific, and thus there is a need to identify specific immunological pathways that could be targeted to treat this disease. EoE is associated with polymorphisms in the gene that encodes thymic stromal lymphopoietin (TSLP), a cytokine that promotes allergic inflammation, but how TSLP might contribute to EoE disease pathogenesis has been unclear. Here, we describe a new mouse model of EoE-like disease that developed independently of IgE, but was dependent on TSLP and basophils, as targeting TSLP or basophils during the sensitization phase limited disease. Notably, therapeutic TSLP neutralization or basophil depletion also ameliorated established EoE-like disease. In human subjects with EoE, we observed elevated TSLP expression and exaggerated basophil responses in esophageal biopsies, and a gain-of-function TSLP polymorphism was associated with increased basophil responses in patients with EoE. Together, these data suggest that the TSLP-basophil axis contributes to the pathogenesis of EoE and could be therapeutically targeted to treat this disease.

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.

Immune circuits in asthma

Asthma is an inflammatory disorder of the conducting airways that has traditionally been classified according to severity. While this has been helpful in guiding treatment with drugs that are currently available such as β2-adrenoceptor agonists and corticosteroids, it takes little account of disease heterogeneity and causal pathways. This review draws attention to subphenotypes of asthma involving different mechanisms and moves the focus away from the adaptive immune response more towards innate immune mechanisms. This mandates a new view of the disease in which causal pathways linked to biomarkers are found and treatments targeted to these pathways as described in a more personalised approach to medicine.

A consideration of biomarkers to be used for evaluation of inflammation in human nutritional studies

To monitor inflammation in a meaningful way, the markers used must be valid: they must reflect the inflammatory process under study and they must be predictive of future health status. In 2009, the Nutrition and Immunity Task Force of the International Life Sciences Institute, European Branch, organized an expert group to attempt to identify robust and predictive markers, or patterns or clusters of markers, which can be used to assess inflammation in human nutrition studies in the general population. Inflammation is a normal process and there are a number of cells and mediators involved. These markers are involved in, or are produced as a result of, the inflammatory process irrespective of its trigger and its location and are common to all inflammatory situations. Currently, there is no consensus as to which markers of inflammation best represent low-grade inflammation or differentiate between acute and chronic inflammation or between the various phases of inflammatory responses. There are a number of modifying factors that affect the concentration of an inflammatory marker at a given time, including age, diet and body fatness, among others. Measuring the concentration of inflammatory markers in the bloodstream under basal conditions is probably less informative compared with data related to the concentration change in response to a challenge. A number of inflammatory challenges have been described. However, many of these challenges are poorly standardised. Patterns and clusters may be important as robust biomarkers of inflammation. Therefore, it is likely that a combination of multiple inflammatory markers and integrated readouts based upon kinetic analysis following defined challenges will be the most informative biomarker of inflammation.

Early-life environmental determinants of allergic diseases and the wider pandemic of inflammatory noncommunicable diseases

The unparalleled burden of a diverse range of chronic noncommunicable diseases (NCDs) is a major global challenge in the 21st century. Chronic low-grade inflammation is a common feature of virtually all NCDs, indicating a central role of the immune system. Furthermore, as the most common and earliest-onset NCD, the epidemic of allergic diseases points to specific vulnerability of the developing immune system to modern environmental change. Indeed, many environmental risk factors implicated in the rise of other NCDs have been shown to mediate their effects through immune pathways. The innate immune system provides a clear example of this convergence, with evidence that physical activity, nutrition, pollutants, and the microbiome all influence systemic inflammation through Toll-like receptor pathways (notably Toll-like receptor 4), with downstream effects on the risk of insulin resistance, obesity, cardiovascular risk, immune diseases, and even mood and behavior. Common risk factors will likely mean common solutions, and interdisciplinary strategies to promote immune health should be an integral part of NCD prevention, with a greater focus early in the life course before disease processes are established. In this context allergic disease provides a very important early target to assess the effectiveness of environmental strategies to reduce immune dysregulation.

Gate-keeper function of the intestinal epithelium

There is currently a major focus on the role of the gut barrier function in balancing mucosal immune responses. Increased epithelial permeability for exogenous antigens is a crucial primary or secondary event in the pathogenesis of several disorders affecting body surfaces and beyond. The epithelial gate-keeper function is determined by the individual's age (e.g. preterm vs. term infant), diet, genetics, mucus composition, interactions between mast cells, nerves and neuropeptides, concurrent infection, the commensal microbiota and the epithelium-shielding effect of secretory IgA (SIgA) antibodies provided by breast milk or produced in the individual's gut. The integrity of the epithelial barrier furthermore depends on homeostatic regulatory mechanisms, including mucosal induction of regulatory T cells, where commensal microbiota-host interactions apparently play decisive roles. Thus, both extrinsic and intrinsic factors have been identified that may have an impact on the dynamics of the epithelial cell-cell junctions in the gut and thereby increase or reduce paracellular permeability. Experiments have shown that SIgA normally cooperates with innate defence factors to protect the epithelium and reinforce its barrier function. In the absence of SIgA commensal gut bacteria overstimulate innate epithelial immunity at the expense of expression of genes that regulate fat and carbohydrate metabolism, resulting in an epithelial gene signature that correlates with the development of lipid malabsorption. This shows that the intestinal epithelial barrier is a cross-road between defence and nutrition, and that SIgA is essential to keep the balance between these two functions.

Gene-environment interactions in asthma and allergic diseases: challenges and perspectives

The concept of gene-environment (GxE) interactions has dramatically evolved in the last century and has now become a central theme in studies that assess the causes of human disease. Despite the numerous efforts to discover genes associated in asthma and allergy through various approaches, including the recent genome-wide association studies, investigation of GxE interactions has been mainly limited to candidate genes, candidate environmental exposures, or both. This review discusses the various strategies from hypothesis-driven strategies to the full agnostic search of GxE interactions with an illustration from recently published articles. Challenges raised by each piece of the puzzle (ie, phenotype, environment, gene, and analysis of GxE interaction) are put forward, and tentative solutions are proposed. New perspectives to integrate various types of data generated by new sequencing technologies and to progress toward a systems biology approach of disease are outlined. The future of a molecular network-based approach of disease to which GxE interactions are related requires space for innovative and multidisciplinary research. Assembling the various parts of a puzzle in a complex system could well occur in a way that might not necessarily follow the rules of logic.

The role of Helicobacter pylori infection in the development of allergic asthma

Asthma is one of the most prevalent chronic diseases in developed countries, with steady increases in asthma prevalence evident, particularly in the last few decades. As genetic factors are unlikely to contribute to the rise in asthma prevalence, changes in lifestyle and exposure to environmental stimuli have been proposed to account for this trend. The 'disappearing microbiota' hypothesis postulates that major shifts in the human microbiome, resulting from dramatic lifestyle changes, account for the increase in asthma prevalence. In this context, persistent gastric colonization with the human-specific pathogen Helicobacter pylori has been negatively associated with the occurrence of asthma in epidemiological studies. In addition, experimental models of allergic airway disease revealed a direct link between infection with H. pylori and suppression of allergic airway disease through the induction of regulatory T cells. These and other new insights hold the promise of opening up new avenues toward the development of innovative, new strategies directed at asthma treatment and prevention.

Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease

BACKGROUND

Deviations in composition and diversity of intestinal microbiota in infancy have been associated with both the development and recurrence of atopic eczema. Thus, we decided to use a deep and global microarray-based method to characterize the diversity and temporal changes of the intestinal microbiota in infancy and to define specific bacterial signatures associated with eczema. Faecal microbiota at 6 and 18 months of age were analysed from 34 infants (15 with eczema and 19 healthy controls) selected from a prospective follow-up study based on the availability of faecal samples. The infants were originally randomized to receive either Lactobacillus rhamnosus GG or placebo.

RESULTS

Children with eczema harboured a more diverse total microbiota than control subjects as assessed by the Simpson's reciprocal diversity index of the microarray profiles. Composition of the microbiota did not differ between study groups at age of 6 months, but was significantly different at age of 18 months as assessed by MCPP (p=0.01). At this age healthy children harboured 3 -fold greater amount of members of the Bacteroidetes (p=0.01). Microbiota of children suffering from eczema had increased abundance of the Clostridium clusters IV and XIVa, which are typically abundant in adults. Probiotic Lactobacillus rhamnosus GG supplementation in early infancy was observed to have minor long-term effects on the microbiota composition.

CONCLUSION

A diverse and adult-type microbiota in early childhood is associated with eczema and it may contribute to the perpetuation of eczema.

Probiotics in the development and treatment of allergic disease

Gut microbiota composition can discriminate between allergic and healthy children, and the distinction may precede clinical manifestations of disease. The mother provides the first inoculum of bacteria, which influences the risk of becoming allergic later in life. Bifidobacterium species are major determinants of disease risk. Specific probiotics may modulate early microbial colonization, which represents the first intervention target in allergic disease, together with their ability to reverse the increased intestinal permeability characteristic of children with atopic eczema and food allergy. Probiotics also enhance gut-specific IgA responses, which are frequently defective in children with food allergy. In addition, probiotics have the potential to alleviate allergic inflammation locally and systemically.

Epigenetics in inflammatory bowel disease

PURPOSE OF REVIEW

To briefly summarize some of the principles of epigenetics and assess their potential relevance for the disease pathogenesis of inflammatory bowel diseases (IBDs). To review the results of recent IBD-related epigenetic studies, discuss main challenges as well as highlight the opportunities for future research in this field.

RECENT FINDINGS

Evidence is accumulating for a major role of epigenetic mechanisms in the disease pathogenesis of several immune-mediated diseases. Recent findings indicate that epigenetics may mediate some of the effects of environment, genetic predisposition and intestinal microbiota on IBD pathogenesis.

SUMMARY

Epigenetics is a rapidly expanding and hugely promising area of research. At best, it may provide a unifying molecular mechanism to explain complex immune-mediated diseases such as IBD. Future research studies must be carefully designed, performed and analysed taking into account the basic principles of epigenetics in order to ensure the true potential of this field is realized in the understanding of IBD.

ADAMTS-12 metalloprotease is necessary for normal inflammatory response

ADAMTSs (a disintegrin and metalloprotease with thrombospondin domains) are a family of enzymes with both proteolytic and protein interaction functions, which have been implicated in distinct pathologies. In this work, we have investigated the putative role of ADAMTS-12 in inflammation by using a mouse model deficient in this metalloprotease. Control and mutant mice were subjected to different experimental conditions to induce colitis, endotoxic sepsis, and pancreatitis. We have observed that Adamts12-deficient mice exhibit more severe inflammation and a delayed recovery from these challenges compared with their wild-type littermates. These changes are accompanied by an increase in inflammatory markers including several cytokines, as assessed by microarray expression analysis and proteomic-based approaches. Interestingly, the clinical symptoms observed in Adamts12-deficient mice are also concomitant with an elevation in the number of neutrophils in affected tissues. Finally, isolation and in vitro culture of human neutrophils demonstrate that the presence of ADAMTS-12 induces neutrophil apoptosis. On the basis of these results, we propose that ADAMTS-12 is implicated in the inflammatory response by modulating normal neutrophil apoptosis.

Reference values of impulse oscillometry and its utility in the diagnosis of asthma in young Korean children

AIMS

The aims of this study were (1) to determine the reference values for impulse oscillometry (IOS) and (2) to apply them to the evaluation of asthma in the general population of young Korean children.

METHODS

We performed a questionnaire survey and IOS measurements in 390 children aged 3-7 years in Seoul and Gyeonggi province, Korea, from July to August 2010. IOS measurements included respiratory resistance (Rrs) and respiratory reactance (Xrs) at 5, 10, 15, 20, 25, and 35 Hz, respiratory impedance (Zrs), and resonance frequency (RF) before and 15 min after inhalation of 200 μg salbutamol. To determine the reference values for IOS, 161 children defined as healthy controls were assessed.

RESULTS

The IOS measurements were presented as means and standard deviations. The reference equations for IOS variables were determined by multiple linear regression analysis taking into account their height, weight, and age (R5 = 2.242 - 0.008 × height (cm) - 0.005 × age (months), coefficients of determination (R(2)) = 0.213). Height had the greatest correlation with IOS variables, similar to previous studies. Positive airway obstruction was defined as R5 greater than the 95th percentile of predicted R5 from the reference equation. There was a higher percentage of children with positive airway obstruction in children with asthma than in healthy controls (27.3% vs. 6.2%). Multivariate logistic regression analysis indicated that positive airway obstruction was a significant risk factor for the diagnosis of asthma (adjusted odds ratio (aOR), 6.245; 95% confidence interval (CI), 2.270-17.175).

CONCLUSION

This study provided reference values for IOS in young Korean children and applied the reference values to evaluate children with asthma. We suggest the 95th percentile of predicted R5 as a cut-off value for positive airway obstruction, which may increase the risk for diagnosis of asthma.

Critical review: vegetables and fruit in the prevention of chronic diseases

BACKGROUND

Vegetables and fruit provide a significant part of human nutrition, as they are important sources of nutrients, dietary fibre, and phytochemicals. However, it is uncertain whether the risk of certain chronic diseases can be reduced by increased consumption of vegetables or fruit by the general public, and what strength of evidence has to be allocated to such an association.

METHODS

Therefore, a comprehensive analysis of the studies available in the literature and the respective study results has been performed and evaluated regarding obesity, type 2 diabetes mellitus, hypertension, coronary heart disease (CHD), stroke, cancer, chronic inflammatory bowel disease (IBD), rheumatoid arthritis (RA), chronic obstructive pulmonary disease (COPD), asthma, osteoporosis, eye diseases, and dementia. For judgement, the strength of evidence for a risk association, the level of evidence, and the number of studies were considered, the quality of the studies and their estimated relevance based on study design and size.

RESULTS

For hypertension, CHD, and stroke, there is convincing evidence that increasing the consumption of vegetables and fruit reduces the risk of disease. There is probable evidence that the risk of cancer in general is inversely associated with the consumption of vegetables and fruit. In addition, there is possible evidence that an increased consumption of vegetables and fruit may prevent body weight gain. As overweight is the most important risk factor for type 2 diabetes mellitus, an increased consumption of vegetables and fruit therefore might indirectly reduces the incidence of type 2 diabetes mellitus. Independent of overweight, there is probable evidence that there is no influence of increased consumption on the risk of type 2 diabetes mellitus. There is possible evidence that increasing the consumption of vegetables and fruit lowers the risk of certain eye diseases, dementia and the risk of osteoporosis. Likewise, current data on asthma, COPD, and RA indicate that an increase in vegetable and fruit consumption may contribute to the prevention of these diseases. For IBD, glaucoma, and diabetic retinopathy, there was insufficient evidence regarding an association with the consumption of vegetables and fruit.

CONCLUSIONS

This critical review on the associations between the intake of vegetables and fruit and the risk of several chronic diseases shows that a high daily intake of these foods promotes health. Therefore, from a scientific point of view, national campaigns to increase vegetable and fruit consumption are justified. The promotion of vegetable and fruit consumption by nutrition and health policies is a preferable strategy to decrease the burden of several chronic diseases in Western societies.

IFN-λ and IgE-mediated allergic disease: a potential future role?

Reduced early microbial exposure has become a leading candidate to explain the rise in allergic disease, and research has focused on studying the interaction between the developing immune system and the microbial environment. However, despite intense interest, the pathways that lead to dysregulation of the immune system in allergic disease are still poorly understood. The newly described type III IFN-λ molecules were initially shown to exhibit antiviral activity, but these molecules are also likely to have an important role to play in the immune-epithelial interface, given their immunomodulatory functions and restricted receptor expression to immune and epithelial cells. Previous studies on the role of IFN-λ in allergic disease have been limited to allergic asthma. More recently, a genetic variation flanking IL28B encoding IFN-λ3 has been associated with allergic disease. Here, we examine this family and suggest how IFN-λ may be an important player in allergic disease.

Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence

Healthy functioning is an emergent property of the network of interacting biomolecules that comprise an organism. It follows that disease (a network shift that causes malfunction) is also an emergent property, emerging from a perturbation of the network. On the one hand, the biomolecular network of every individual is unique and this is evident when similar disease-producing agents cause different individual pathologies. Consequently, a personalized model and approach for every patient may be required for therapies to become effective across mankind. On the other hand, diverse combinations of internal and external perturbation factors may cause a similar shift in network functioning. We offer this as an explanation for the multi-factorial nature of most diseases: they are "systems biology diseases," or "network diseases." Here we use neurodegenerative diseases, like Parkinson's disease (PD), as an example to show that due to the inherent complexity of these networks, it is difficult to understand multi-factorial diseases with simply our "naked brain." When describing interactions between biomolecules through mathematical equations and integrating those equations into a mathematical model, we try to reconstruct the emergent properties of the system in silico. The reconstruction of emergence from interactions between huge numbers of macromolecules is one of the aims of systems biology. Systems biology approaches enable us to break through the limitation of the human brain to perceive the extraordinarily large number of interactions, but this also means that we delegate the understanding of reality to the computer. We no longer recognize all those essences in the system's design crucial for important physiological behavior (the so-called "design principles" of the system). In this paper we review evidence that by using more abstract approaches and by experimenting in silico, one may still be able to discover and understand the design principles that govern behavioral emergence.

Perinatal maternal administration of Lactobacillus paracasei NCC 2461 prevents allergic inflammation in a mouse model of birch pollen allergy

BACKGROUND

The hygiene hypothesis implies that microbial agents including probiotic bacteria may modulate foetal/neonatal immune programming and hence offer effective strategies for primary allergy prevention; however their mechanisms of action are poorly understood. We investigated whether oral administration of Lactobacillus paracasei NCC 2461 to mothers during gestation/lactation can protect against airway inflammation in offspring in a mouse model of birch pollen allergy, and examined the immune mechanisms involved.

METHODS

BALB/c mice were treated daily with L. paracasei in drinking water or drinking water alone in the last week of gestation and during lactation. Their offspring were sensitized with recombinant Bet v 1, followed by aerosol challenge with birch pollen extract.

RESULTS

Maternal exposure to L. paracasei prevented the development of airway inflammation in offspring, as demonstrated by attenuation of eosinophil influx in the lungs; reduction of IL-5 levels in bronchoalveolar lavage, and in lung and mediastinal lymph node cell cultures; and reduced peribronchial inflammatory infiltrate and mucus hypersecretion. While allergen-specific IgE and IgG antibody levels remained unchanged by the treatment, IL-4 and IL-5 production in spleen cell cultures were significantly reduced upon allergen stimulation in offspring of L. paracasei treated mice. Offspring of L. paracasei supplemented mothers had significantly reduced Bet v 1-specific as well as Concanavalin A-induced responses in spleen and mesenteric lymph node cell cultures, suggesting the modulation of both antigen-specific and mitogen-induced immune responses in offspring. These effects were associated with increased Foxp3 mRNA expression in the lungs and increased TGF-beta in serum.

CONCLUSION

Our data show that in a mouse model of birch pollen allergy, perinatal administration of L. paracasei NCC 2461 to pregnant/lactating mothers protects against the development of airway inflammation in offspring by activating regulatory pathways, likely through TLR2/4 signalling.

Protective effects of cathelicidin-encoding Lactococcus lactis in murine ulcerative colitis

BACKGROUND AND AIM

Intrarectal administration of mouse cathelin-related antimicrobial peptide (mCRAMP) reduced intestinal inflammation in mice. In the current study, we examined whether mCRAMP-transformed Lactococcus lactis given orally attained similar protective effects.

METHOD

mCRAMP was produced and secreted from the transformed L. lactis. Murine colitis was induced by ingestion of 3% dextran sulfate sodium (DSS) for 7 days. Eight or 10 log colony forming unit (cfu) L. lactis or the transformed strains with or without nisin induction were given orally as a parallel treatment with DSS. The body weight, fecal microbiota populations, clinical symptoms and histological examinations of colonic tissues were determined. Myeloperoxidase (MPO) activity and malondialdehyde (MDA) level were also evaluated to reflect the degree of inflammation. A prototype anti-inflammatory drug sulfasalazine was used as a reference drug to compare the efficacy and mechanisms of action for ulcerative colitis (UC).

RESULT

Compared with the control group with colitis, cathelicidin-transformed L. lactis could improve the clinical symptoms, maintain crypt integrity and preserve mucus content (P < 0.01). The number of apoptotic cells, MPO activity and MDA level were also significantly reduced (P < 0.05). The increases of fecal microbiota in colitis animals were markedly prevented (P < 0.001). Unlike mCRAMP-encoding L. lactis, effective doses of sulfasalazine only alleviated the clinical symptoms (P < 0.01) but not the mucosal damage in the colon.

CONCLUSION

mCRAMP-transformed L. lactis has been shown to produce mCRAMP, effectively preventing murine UC. Oral administration of this biological preparation is better than sulfasalazine for the treatment of UC.

Primary biliary cirrhosis: a multi-faced interactive disease involving genetics, environment and the immune response

Primary biliary cirrhosis (PBC) is considered a model autoimmune disease based on several features, including the presence of a highly directed and very specific immune response to mitochondrial autoantigens, a female predominance, a targeted destruction of the biliary epithelium, and homogeneity between patients. It is essentially a chronic progressive cholestatic liver disease characterized by immune-mediated destruction of small- and medium-sized intrahepatic bile ducts. There is considerable variation in the incidence and prevalence of the disease between regions of the world, although such differences likely reflect not only a true disparity in disease but also differences in awareness; for example, in the United States, PBC is often detected in an asymptomatic stage based on multi-phasic clinical testing. There has been considerable progress at defining the immune response in this disease, including quantitation of autoreactive T cells against PDC-E2, the major mitochondrial autoantigen. The overwhelming data suggests that patients develop PBC based on a genetic predisposition and loss of tolerance to one or more environmental agents. In this review, we will present an updated overview of PBC and place it in the context of autoimmunity.

Gene-environment interaction in chronic disease: a European Science Foundation Forward Look

Over the last half century, a dramatic increase in the incidence of chronic inflammatory diseases, such as asthma, allergy, and irritable bowel syndrome, has rightfully led to concern about how the modern lifestyle might inappropriately trigger innate physiologic defense mechanisms. Health care research in the Western world is faced with a significant challenge if it is to meet the needs of its populations in the decades ahead. The tools with which we hope to advance our understanding of the intrinsic and extrinsic mechanisms of chronic inflammatory diseases must therefore be adequately exploited and further developed to identify treatment and prevention strategies. There is an urgent need to prioritize resources and identify the most efficient scientific and societal initiatives to be adopted within this area. In this context national collaboration within Europe and beyond to establish state-of-the-art practices with an interdisciplinary perspective and promote an efficient exchange of best practices is essential. Such an approach likely represents the most efficient manner in which strategies for amelioration of the increase of chronic inflammatory diseases in the Western world can be achieved. The present report is based on a Forward Look initiative conducted by the European Medical Research Councils under the European Science Foundation. Experts from industry and academia, as well as relevant interest organizations, have been consulted in the process of conducting this initiative and have, based on this work, developed a set of final recommendations that target academic research, science funders, and policy makers.

Genetic variations in IL28B and allergic disease in children

Environmental changes affecting the relationship between the developing immune system and microbial exposure have been implicated in the epidemic rise of allergic disease in developed countries. While early developmental differences in T cell function are well-recognised, there is now emerging evidence that this is related to developmental differences in innate immune function. In this study we sought to examine if differences associated with innate immunity contribute to the altered immune programming recognised in allergic children. Here, we describe for the first time, the association of carriage of the T allele of the tagging single nucleotide polymorphism rs12979860 3 kb upstream of IL28B, encoding the potent innate immune modulator type III interferon lambda (IFN-λ3), and allergy in children (p = 0.004; OR 4.56). Strikingly, the association between rs12979860 genotype and allergic disease is enhanced in girls. Furthermore, carriage of the T allele at rs12979860 correlates with differences in the pro-inflammatory profile during the first five years of life suggesting this contributes to the key differences in subsequent innate immune development in children who develop allergic disease. In the context of rising rates of disease, these immunologic differences already present at birth imply very early interaction between genetic predisposition and prenatal environmental influences.

Helminth-host immunological interactions: prevention and control of immune-mediated diseases

Exposure to commensal and pathogenic organisms strongly influences our immune system. Exposure to helminths was frequent before humans constructed their current highly hygienic environment. Today, in highly industrialized countries, contact between humans and helminths is rare. Congruent with the decline in helminth infections is an increase in the prevalence of autoimmune and inflammatory disease. It is possible that exclusion of helminths from the environment has permitted the emergence of immune-mediated disease. We review the protective effects of helminths on expression of inflammatory bowel disease, multiple sclerosis, and animal models of these and other inflammatory diseases. We also review the immune pathways altered by helminths that may afford protection from these illnesses. Helminth exposure tends to inhibit IFN-γ and IL-17 production, promote IL-4, IL-10, and TGF-β release, induce CD4(+) T cell Foxp3 expression, and generate regulatory macrophages, dendritic cells, and B cells. Helminths enable protective pathways that may vary by specific species and disease model. Helminths or their products likely have therapeutic potential to control or prevent immune-mediated illness.

Glomerular disease in 2011: New clues to environmental influences in glomerular disease

Research into genetic susceptibilities for proteinuric glomerular diseases has uncovered key pathogenic contributions from inheritable defects in podocytes. However, much less is known about environmental factors that may initiate or propagate podocyte injury. Seminal reports in 2011 provided new mechanistic insights into how this may occur.

Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine

The analysis of frailty originated in studies of aging and demography in which the objective was to demonstrate that the hazard rates (mortality risks) of individuals in a population could significantly differ from the population hazard rate as a whole. The differences between these two hazard rates can arise from frailty - differences among individuals that are not observed in a study. We posit that frailty modeling is a useful approach for risk analysis in personalized medicine because it provides a way to address the important and perplexing question of how to translate findings from population studies to the diagnosis and treatment of disease in specific individuals. Our suggestion is based on three unique advantages of frailty modeling: frailty modeling offers an effective approach to analyze the risks at both the individual and population levels and can be used to infer relationships between the two; frailty modeling can be used to analyze the dependence between survival events - one of the most difficult issues in any field that involves common risks; and frailty modeling can be used to describe unobserved or unobservable risks. Finally, we suggest that frailty modeling should be particularly useful in the study and treatment of diseases that are caused or influenced by the human microbiome. By doing so, truly 'personalized' medicine can advance based on a better understanding of the risks to both 'trees' (individuals) and 'forests' (populations).

The new link between gut-brain axis and neuropsychiatric disorders

PURPOSE OF REVIEW

Although the cause of most neuropsychiatric disorders remains uncertain, new data offer alternative explanations warranting further validations. This review summarizes some recent findings that may localize the origin of eating disorders as well as some other neuropsychiatric disorders outside the brain and discuss their cause as a possible dysfunction of the gut-brain axis involving the humoral immune system.

RECENT FINDINGS

The gut microbiota has been identified as the main source of highest biological variability confined in an individual and also provides constant antigenic stimulation shaping up the physiological immune response. Furthermore, molecular mimicry has been shown among microbial proteins including gut microbiota and several key neuropeptides involved in the regulation of motivated behavior and emotion. Immunoglobulins reactive with these neuropeptides have been identified in humans, and their levels or affinities were associated with neuropsychiatric conditions including anxiety, depression, eating and sleep disorders.

SUMMARY

Cross-reacting immunoglobulins may bind both microbial sequences and neuropeptides, thereby constituting a particular way of signaling between the gut and the brain. Alteration of this link may contribute to several neuropsychiatric disorders, emphasizing the key role of nutrition among other factors influencing gut content and intestinal permeability.