Interactions between Genetic Variants of FLG and Chromosome 11q13 Locus Determine Susceptibility for Eczema Phenotypes

Predicting eczema severity beyond childhood

BACKGROUND

We evaluated factors associated with eczema severity in adolescence.

METHODS

Nottingham Eczema Severity Score (NESS), family and personal history of atopy, skin prick test for common food and aeroallergens, highest serum IgE level and eosinophil count were evaluated. Patients with paired NESSs (childhood-NESS is NESS performed at <10 years of age; adolescence-NESS is NESS performed at age >10 years) were further analyzed.

RESULTS

Adolescence-NESS (n=383 patients) was associated with eczema onset in infancy, dust mite and food allergen sensitization, dietary avoidance, use of wet wrap, traditional Chinese medicine, immunomodulant (azathioprine or cyclosporine), high IgE level, eosinophil count, but not with family/personal history of atopy. Eighty-two patients had both childhood-NESS and adolescence-NESS (mean follow-up of 6.8 years) showing that adolescence-NESS was associated with childhood- NESS severity grades (P=0.034). Of these patients, 48% remained in the same severity grades, whereas 39% improved, and 13% deteriorated from childhood to adolescence.

CONCLUSIONS

It is not possible to assure parents that their child can outgrow eczema. In eczema prognosis research, long-term follow-up is warranted.

A roadmap to multifactor dimensionality reduction methods

Complex diseases are defined to be determined by multiple genetic and environmental factors alone as well as in interactions. To analyze interactions in genetic data, many statistical methods have been suggested, with most of them relying on statistical regression models. Given the known limitations of classical methods, approaches from the machine-learning community have also become attractive. From this latter family, a fast-growing collection of methods emerged that are based on the Multifactor Dimensionality Reduction (MDR) approach. Since its first introduction, MDR has enjoyed great popularity in applications and has been extended and modified multiple times. Based on a literature search, we here provide a systematic and comprehensive overview of these suggested methods. The methods are described in detail, and the availability of implementations is listed. Most recent approaches offer to deal with large-scale data sets and rare variants, which is why we expect these methods to even gain in popularity.

Childhood asthma and spirometric indices are associated with polymorphic markers of two vitamin D 25-hydroxylase genes

BACKGROUND

Polymorphic markers of vitamin D pathway genes have been associated with asthma traits in different White populations. This study investigated the relationship between asthma phenotypes and single nucleotide polymorphisms (SNPs) of vitamin D receptor (VDR), vitamin D binding protein (GC), two 25-hydroxylases (CYP2R1 and CYP27A1), and 1α-hydroxylase (CYP27B1) in Hong Kong Chinese children.

METHODS

23 SNPs of the five vitamin D pathway genes were successfully genotyped in 914 asthmatic children and 1231 non-allergic controls. Genotypic and haplotypic associations with asthma phenotypes (diagnosis, spirometric indices, total IgE, and eosinophil percentage) were analyzed by multivariate regression. Generalized multifactor dimensionality reduction was used to detect epistatic interactions between SNPs for asthma phenotypes.

RESULTS

Several SNPs of CYP27A1, CYP27B1, GC, and CYP2R1 were associated with asthma or spirometric indices, although only the association between FEV1 and CYP2R1 rs7935792 passed Bonferroni correction (p = 2.73 × 10(-4) ). Patients with CC genotype of rs7935792 had higher FEV1 than those with the other two genotypes. Asthma was also associated with TT haplotype of CYP27A1 and AGGATA haplotype of CYP2R1 (p = 0.021 and 0.024, respectively). Besides, strong association was found between FEV1 and GATAG of CYP2R1 (β = 13.37, p = 4.83 × 10(-4) ). GMDR failed to identify any 2-locus to 4-locus interaction that modulated asthma or spirometric indices.

CONCLUSIONS

Several SNPs and haplotypes of CYP2R1 are associated with asthma diagnosis and FEV1 in children. Asthma is also modestly associated with a CYP27A1 haplotype. These two 25-hydroxylase genes may be genetic determinants for asthma phenotypes in children.

Vitamin D deficiency is associated with diagnosis and severity of childhood atopic dermatitis

BACKGROUND

Recent studies implicated the importance of vitamin D in innate immune defense and pathogenesis of allergic diseases. However, the impact of vitamin D deficiency on atopic dermatitis (AD) diagnosis and severity remains unclear. This case-control study investigated such relationship in Hong Kong Chinese children.

METHODS

Serum 25-hydroxyvitamin D [25(OH)D] levels of 498 AD children and 328 non-allergic controls were measured by immunoassay. Subjects were categorized into deficient (< 25 nm), insufficient (25-49.9 nm), and sufficient (≥ 50 nm) groups. Short-term and long-term AD severity was evaluated by physician-diagnosed SCORing Atopic Dermatitis (SCORAD) and Nottingham Eczema Severity Score (NESS), respectively. Atopy biomarkers were also measured for analysis.

RESULTS

The mean (s.d.) serum 25(OH)D levels in AD patients and controls were 28.9 (15.3) and 34.2 (14.5) nm, respectively (p < 0.001). More patients had serum 25(OH)D levels <25 nm than controls (47.8% vs. 26.6%). AD severity as indicated by both SCORAD and NESS showed inverse associations with serum 25(OH)D levels (respective p = 3.6 × 10(-4) and 0.004 when adjusted for age, sex, month of assessment, and immunoassay batch as covariates). Vitamin D-deficient patients (3.08 ± 0.76) had higher logarithm-transformed total IgE than those with insufficient (2.74 ± 0.69) and sufficient (2.72 ± 0.72) serum 25(OH)D levels (p < 0.001). The proportion of subjects with elevated IgE was higher in vitamin D-deficient (43.2%) than vitamin D-sufficient (20.0%) groups.

CONCLUSIONS

Vitamin D deficiency and insufficiency are prevalent in Hong Kong Chinese children. Vitamin D deficiency is associated with childhood AD and high total IgE. Serum 25(OH)D levels correlate inversely with both long- and short-term AD severity.

Eczema phenotypes are associated with multiple vitamin D pathway genes in Chinese children

BACKGROUND

Vitamin D is increasingly recognized to play crucial roles in cutaneous immunity, and vitamin D treatment improved eczema control in small clinical trials. Several vitamin D-related genes were associated with asthma, but there are no data for eczema.

METHODS

Twenty-three single-nucleotide polymorphisms (SNPs) of five vitamin D-related genes (CYP27A1, CYP2R1, CYP27B1, GC and VDR) were genotyped in 1442 Chinese children with eczema and 1231 non-allergic controls. SNPs that followed Hardy-Weinberg equilibrium and yielded ≥ 95% genotyping call-rate were included. Haplotypic associations and SNP-SNP interactions for eczema diagnosis and subphenotypes were analysed.

RESULTS

Atopic eczema was associated with rs4674343 of CYP27A1 (odds ratio 0.66, 95% confidence interval 0.53-0.83, P = 0.0004). Increased eosinophil percentage was associated with CYP2R1 rs2060793A (P = 0.001) and rs1933064A (P = 0.001). Two CYP2R1 haplotypes increased eczema risk whereas one VDR haplotype lowered eczema risk. GC rs7041 and CYP2R1 rs7935792 interacted to modulate total IgE (cross-validation consistency 10/10, P = 0.047). Specifically, high-risk eczema patients had higher log-transformed total IgE than low-risk patients (2.76 ± 0.76 vs 2.60 ± 0.80, P = 0.002).

CONCLUSION

A vitamin D-related SNP rs4674343 on CYP27A1 was found to be protective against atopic eczema. CYP2R1 and VDR haplotypes altered eczema susceptibility and eosinophil percentage, and GC and CYP2R1 interacted to determine total IgE among eczema patients.