Network analysis of single nucleotide polymorphisms in asthma

A Polymorphism in the Catalase Gene Promoter Confers Protection against Severe RSV Bronchiolitis

Respiratory syncytial virus (RSV) infection is associated with oxidative lung injury, decreased levels of antioxidant enzymes (AOEs), and the degradation of the transcription factor NF-E2-related factor 2 (NRF2), a master regulator of AOE expression. Single nucleotide polymorphisms (SNPs) in AOE and NRF2 genes have been associated with various lung disorders. To test whether specific NRF2 and/or AOE gene SNPs in children with RSV lower respiratory tract infection were associated with disease severity, one hundred and forty one children <24 month of age with bronchiolitis were assessed for seven AOE and two NRF2 SNPs, and data were correlated with disease severity, which was determined by need of oxygen supplementation and intensive care support. One SNP in the promoter region of the catalase gene, rs1001179, which is associated with higher enzyme expression, was significantly underrepresented (p = 0.01, OR 0.38) among patients with moderate to severe RSV bronchiolitis, suggesting a protective effect against disease severity. Our results suggest that increasing catalase expression/activity could exert a protective role in the context of RSV infection and represent a potential novel therapeutic target to ameliorate viral-induced lung disease.

Importance of Toll-like Receptors in Pro-inflammatory and Anti-inflammatory Responses by Helicobacter pylori Infection

Infectious diseases have been paramount among the threats to human health and survival throughout evolutionary history. Bacterial cell-surface molecules are key factors in the microorganism-host crosstalk, as they can interact with host pattern-recognition receptors (PRRs) of the gastrointestinal mucosa. The best-studied PRRs are toll-like receptors (TLRs). Because TLRs play an important key role in host defense, they have received increasing interest in the evolutionary and population genetics literature, and their variation represents a potential target of adaptive evolution. Helicobacter pylori is one of the commensal bacteria in our body and can have pathogenic properties in a subset of infected people. The history of H. pylori research indicated that humans and bacteria co-evolved during evolution. A genome-wide association study (GWAS) has opened the way for investigating the genomic evolution of bacterial pathogens during the colonization and infection of humans. Recent GWAS research emphasized the importance of TLRs, especially TLR10 during pathogenesis in H. pylori infection. We demonstrated that TLR10, whose ligand was unknown for a long time, can recognize H. pylori LPS. Our results of H. pylori research suggest that TLR10 might play an important role to also recognize other commensal bacteria. In this review, we discuss the importance of TLRs in pro-inflammatory and anti-inflammatory responses by H. pylori infection. Especially, we highlight the TLR10 interaction with H. pylori infection, providing new insights about TLR10 signaling.

Temperature drop and the risk of asthma: a systematic review and meta-analysis

The relationship between asthma and temperature changes remains controversial. The aim of this study was to investigate the association between temperature changes and the risk of asthma. A total of 26 studies (combined total number of subjects N > 26 million), covering 13 countries and Costa Rica, were identified by using a series of keywords in different combinations and searching the papers in PubMed, EMBSEA, Web of Science, MEDLINE, AIM, LILACS, and WPRIM before February 2016. Most of the papers were published in English. Random-effects meta-analyses were performed to evaluate the effect of temperature drop on risk of asthma. Several secondary analyses were also calculated based on stratification for different age, season, latitude, and region on risk of asthma. The odds ratio (OR) estimate between temperature drop and asthma was 1.05 (95% CI 1.02, 1.08) in the meta-analysis. For children, the overall OR was 1.09 (95% CI 1.03, 1.15). Dose-effect analyses showed stronger associations in asthma risk for each 1°1 °C decrement in short-term temperature (OR 1.055, 95% CI 1.00, 1.11). Further stratifications showed that winter (OR 1.03, 95% CI 1.01, 105) and low latitude (OR 1.72, 95% CI 1.23, 2.41) have a statistically significant association with the increased risk of asthma. Exposure of people to short-term temperature drop (per 1 °C decrement) was significantly associated with the risk of lower respiratory tract infections (LRTI) with asthma (OR 1.02, 95% CI 1.00, 1.04). Results suggest an adverse effect of temperature drop on asthma risk, especially in children and low-latitude areas. It may be opportune to consider the preventive actions against temperature drop, including simple face masks, to decrease the risk of asthma.

A case-control study of innate immunity pathway gene polymorphisms in Puerto Ricans reveals association of toll-like receptor 2 +596 variant with asthma

BACKGROUND

For many years, African Dust Storms (ADE) has been thought to be associated with high prevalence of asthma in Puerto Rico (PR). Endotoxins (ENX) have been associated with ADE particulate matter (PM) and are known to promote pro-inflammatory responses in lung cells of susceptible individuals through the Toll-like receptor (TLR2/4) signaling pathways. Genetic variants are plausible contributors to such susceptibility. Therefore, we have evaluated a series of nine single nucleotide polymorphisms (SNPs) in TLR genes, which have been correlated positive and negatively to asthma prevalence and/or risk, in the Puerto Rican asthmatic population.

METHODS

The following SNPs were evaluated in 62 asthmatics and 61 controls through Taqman® Real Time PCR Assay: TLR4 (+896A/G, +1196C/T, -6687A/G); TLR2 (+596C/T, -16934 T/A, +399A/G, +1349C/T) and CD14 (-159C/T, +1188C/G). Genotypes were assessed for asthma association employing an odds ratio (OR) analysis.

RESULTS

Minor allele frequencies (n = 123) were determined for those variants as 0.07, 0.06, 0.35, 0.35, 0.37, 0.29, 0.04, 0.35 and 0.11, respectively. Two (+596C/T, +399A/G) TLR2 SNPs showed to be more represented in the asthmatic group by 89 % and 65 %, respectively. TLR4 SNP +896A/G analysis revealed only 1 G/G genotype (2 %) on the asthmatic group. The CD14 SNPs were similarly represented in the Puerto Rican population. Only the TLR2 +596 SNP was found to be significantly associated to asthma (OR = 3.24 for CT, 2.71 for TT) and particularly to females.

CONCLUSIONS

The identification of TLR SNPs will reveal potential candidates for gene-environment interactions in Puerto Ricans. As far as we know this is the first study to evaluate this type of TLR gene polymorphisms in Puerto Rican asthmatics, contributing to the current knowledge in the Hispanic population.

mRNA-Mediated Gene Supplementation of Toll-Like Receptors as Treatment Strategy for Asthma In Vivo

Asthma is the most common chronic disease in childhood. Although several therapeutic options are currently available to control the symptoms, many drugs have significant side effects and asthma remains an incurable disease. Microbial exposure in early life reduces the risk of asthma and several studies have suggested protective effects of Toll-like receptor (TLR) activation. We showed previously that modified mRNA provides a safe and efficient therapeutic tool for in vivo gene supplementation. Since current asthma drugs do not take patient specific immune and TLR backgrounds into consideration, treatment with tailored mRNA could be an attractive approach to account for the patient's individual asthma phenotype. Therefore, we investigated the effect of a preventative treatment with combinations of Tlr1, Tlr2 and Tlr6 mRNA in a House Dust Mite-induced mouse model of asthma. We used chemically modified mRNA which is-in contrast to conventional viral vectors-non-integrating and highly efficient in gene transfer. In our study, we found that treatment with either Tlr1/2 mRNA or Tlr2/6 mRNA, but not Tlr2 mRNA alone, resulted in better lung function as well as reduced airway inflammation in vivo. The present results point to a potentially protective effect of TLR heterodimers in asthma pathogenesis.

Recurrent wheezing in children

Recurrent wheezing have a significant morbidity and it's estimated that about one third of school-age children manifest the symptom during the first 5 years of life. Proper identification of children at risk of developing asthma at school age may predict long-term outcomes and improve treatment and preventive approach, but the possibility to identify these children at preschool age remains limited. For many years authors focused their studies to identify early children with recurrent wheezing at risk to develop asthma at school age. Different phenotypes have been proposed for a more precise characterization and a personalized plan of treatment. The main criticism concerns the inability to define stable phenotypes with the risk of overestimating or underestimating the characteristics of symptoms in these children. The aim of this review is to report the recent developments on the diagnosis and treatment of recurrent paediatric wheezing.

Systems biology approaches to enhance our understanding of drug hypersensitivity reactions

Hypersensitivity drug reactions (HDRs) encompass a wide spectrum of unpredictable clinical entities. They represent an important health problem, affecting people of all ages, and lead to a large strain on the public health system. Here, we summarize experiments that use high-throughput genomics technologies to investigate HDRs. We also introduce the field of systems biology as a relatively recent discipline concerned with the integration and analysis of high-throughput data sets such as DNA microarrays and next-generation sequencing data. We describe previous studies that have applied systems biology techniques to related fields such as allergy and asthma. Finally, we present a number of potential applications of systems biology to the study of HDRs, in order to make the reader aware of the types of analyses that can be performed and the insights that can be gained through their application.

Early childhood wheezers: identifying asthma in later life

Wheeze in young children is common, and asthma is the most common noncommunicable disease in children. Prevalence studies of recurrent asthma-like symptoms in children under the age of 5 years have reported that one third of children in the US and Europe are affected, and rates and severity appear to be higher in developing countries. Over the last few decades, significant research efforts have focused on identification of risk factors and predictors of wheeze and on tools to identify which children who wheeze will progress to develop asthma. We reviewed the phenotypes of childhood wheezing, genetic risk factors, environmental factors, testing/predictive indices, and primary prevention. While it is generally agreed that a complex interaction of environmental exposure and genetic susceptibility contributes to the development of asthma, limitations in predictive tools and tests restrict our ability to provide families with guidance as to whether their child with wheeze will ultimately develop asthma. Additional research is needed to clarify childhood wheeze phenotypes, to develop tools to determine which children will develop asthma, and to determine how and when to intervene. If these areas can be addressed, it would help reduce this large burden on children, families, and society.

The study of severe cutaneous drug hypersensitivity reactions from a systems biology perspective

PURPOSE OF REVIEW

Stevens-Johnson syndrome and toxic epidermal necrolysis are severe hypersensitivity reactions, the majority of which are drug induced. The underlying mechanisms are not fully understood. Here, we review recent findings concerning both mechanistic and genetic factors related to these diseases and propose future approaches to unravel their complexity.

RECENT FINDINGS

Genome-wide association study studies have identified several variants in the human leukocyte antigen region associated with these reactions. These are highly dependent on the population studied and the triggering drug. The T-cell receptor repertoire of the patient is also key. Fas-Fas ligand interactions, perforin and granulysin have also been identified as important players. Furthermore, a high-throughput gene expression study has identified a number of genes that increase in expression in patients during the acute phase of these reactions.

SUMMARY

We review recent high-throughput studies on these diseases and suggest ways in which the data can be combined and reanalyzed using integrative systems biology techniques. We also suggest future lines of research using recent technology that could shed further light on their underlying mechanisms.

Unravelling adverse reactions to NSAIDs using systems biology

We introduce the reader to systems biology, using adverse drug reactions (ADRs), specifically hypersensitivity reactions to multiple non-steroidal anti-inflammatory drugs (NSAIDs), as a model. To disentangle the different processes that contribute to these reactions - from drug intake to the appearance of symptoms - it will be necessary to create high-throughput datasets. Just as crucial will be the use of systems biology to integrate and make sense of them. We review previous work using systems biology to study related pathologies such as asthma/allergy, and NSAID metabolism. We show examples of their application to NSAIDs-hypersensitivity using current datasets. We describe breakthroughs in high-throughput technology and speculate on their use to improve our understanding of this and other drug-induced pathologies.

Systems biology approach for subtyping asthma; where do we stand now?

PURPOSE OF REVIEW

The purpose of this review is to discuss the present systems biology approach to asthma and how it is helping to define asthma subtypes. Although the general concept of systems biology will be discussed, the article will focus on recent developments in the field related to asthma.

RECENT FINDINGS

The most recent work in systems biology and asthma has occurred in the area of genomics (e.g., pharmacogenomics and gene-environment interactions), protein interaction networks [e.g., interleukin (IL)-33/IL-1 receptor-like 1 signaling], cluster analysis of asthma patients (e.g., application of severe asthma research program clusters to a general urban asthma population), and multiscale approaches to asthma encompassing data from the molecule to whole organ (e.g., modeling of airways hyperresponsiveness).

SUMMARY

The results of recent work in this area have led to new insight into gene-cytokine and protein-protein networks involved in asthma, a better determination of key clinical factors associated with asthma subtypes, and the beginning of sophisticated multiscale approaches to modeling, understanding and predicting the behavior of the asthmatic lung.

Proposed model for Iranian national system of registration of allergy and asthma

Introduction:

Asthma and allergies in addition to demanding social costs–the economic community, one of the major causes of morbidity and mortality in the world is considered. In the last decade in Iran despite the positive developments in many areas of health records into categories based asthma and allergy international standards, less attention has been paid. Improving the quality of care system, identifying groups at risk of asthma and allergies, control plan, prevention and assessment of asthma and allergies due to possible that when allergy and asthma information registration system and create the complete and timely data to be collected. Considering now an efficient national system of registration allergy and asthma that can meet the health needs can no need for this study was felt.

Materials and Methods:

This study, study–the comparison was done in the years 2010-2011. In this research, using library resources, information networks and consultations with experts inside the country gathered on the main axis and branches of national registration system, asthma and allergies in American countries–Australia and England were examined and given economic conditions, cultural and geographical themes for our records system, the axes were proposed objectives, structure, data elements, standard registration process? Data and classification systems are given.

Results:

The proposed model for national registration system, asthma and allergies in the country is shown in a table. In this table the proposed system based on six main “targets”, “structure”, “data elements”, “data collection process,” “registration criteria” and “classification system” is designed.

Conclusion:

The results and recommendations to the International Institute for asthma and allergies, reduction in low registers, and can increase the quality of the proposed model, including advantages in comparison with the existing system of the country noted.

Strategies for molecular classification of asthma using bipartite network analysis of cytokine expression

Asthma is a chronic inflammatory disease of the airways that leads to various degrees of recurrent respiratory symptoms affecting patients globally. Specific subgroups of asthma patients have severe disease leading to increased healthcare costs and socioeconomic burden. Despite the overwhelming prevalence of the asthma, there are limitations in predicting response to therapy and identifying patients who are at increased risk of morbidity. This syndrome presents with common clinical signs and symptoms; however, awareness of subgroups of asthma patients with distinct characteristics has surfaced in recent years. Investigators attempt to describe the phenotypes of asthma to ultimately assist with diagnostic and therapeutic applications. Approaches to asthma phenotyping are multifold; however, it can be partitioned into 2 essential groups, clinical phenotyping and molecular phenotyping. Innovative techniques such as bipartite network analysis and visual analytics introduce a new dimension of data analysis to identify underlying mechanistic pathways.