IL1B genetic variation and plasma C-reactive protein level among young adults: the CARDIA study

Translational Metabolomics: Current Challenges and Future Opportunities

Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most importantly, metabolomics studies have produced great breakthroughs in biomarker discovery, identification of novel metabolites and more detailed characterisation of biological pathways in many organisms. However, translation of the research outcomes into clinical tests and user-friendly interfaces has been hindered due to many factors, some of which have been outlined hereafter. This position paper is the summary of discussion on translational metabolomics undertaken during a peer session of the Australian and New Zealand Metabolomics Conference (ANZMET 2018) held in Auckland, New Zealand. Here, we discuss some of the key areas in translational metabolomics including existing challenges and suggested solutions, as well as how to expand the clinical and industrial application of metabolomics. In addition, we share our perspective on how full translational capability of metabolomics research can be explored.

Cytokine polymorphisms are associated with daytime napping in adults living with HIV

OBJECTIVE/BACKGROUND

Daytime napping longer than one hour has been associated with an increased risk for all-cause mortality. Associations between cytokine polymorphisms and daytime napping in chronic illnesses such as HIV, however, have not been well described. The purpose of this study was to examine cytokine polymorphisms associated with long daytime napping in adults living with HIV.

METHODS

A cross-sectional analysis was conducted using a convenience sample of 257 adults living with HIV. Daytime napping was assessed with wrist actigraphy data collected over three days. Participants categorized as long nappers (≥60 min) were compared to short nappers and non-nappers (<60 min). Single nucleotide polymorphisms (SNPs) for 15 candidate genes involved in cytokine signaling were analyzed. Genes included: interferon-gamma (IFNG), IFNG receptor 1 (IFNGR1), interleukins (IL1B, IL1R, IL1R2, IL2, IL4, IL6, IL8, IL10, IL13, IL17A), nuclear factors of kappa light polypeptide gene enhancer in B cells (NFKB1 and NFKB2), and tumor necrosis factor alpha (TNFA).

RESULTS

After adjusting for relevant demographic and clinical characteristics, long daytime napping was associated with 12 SNPs from seven genes: 1) IFNG rs2069728; 2) IL1B rs1143642, rs1143627, and rs16944; 3) IL2 rs2069763; 4) IL6 rs4719714, rs1554606, and rs2069845; 5) IL17A rs3819024 and rs8193036; 6) NFKB1 rs4648110; and 7) NFKB2 rs1056890.

CONCLUSIONS

Cytokine genetic variations may have a role in physiological regulation of daytime napping as well as nocturnal sleep. Cytokine polymorphisms associated with long daytime napping could help identify adults with HIV who may benefit from targeted therapeutic interventions.

Adipokine Gene Single-Nucleotide Polymorphisms in Portuguese Obese Adolescents: Associations with Plasma Concentrations of Adiponectin, Resistin, IL-6, IL-1β, and TNF-α

BACKGROUND

The genetic contribution to obesity and to circulating adipokine levels has not been completely clarified. We aimed to evaluate adipokine genes' single-nucleotide polymorphism (SNP) prevalence and its association with circulating adipokine levels and risk factors for cardiovascular disease in an obese Portuguese pediatric population.

METHODS

Two hundred forty-eight obese adolescents (mean age 13.4 years old; 47.2% females) participated in a cohort study. We screened 12 SNPs by direct sequencing in five adipokine genes: adiponectin (ADIPOQ: rs16861194, rs17300539, rs266729, rs2241766, rs1501299), interleukin-1β (IL-1β; rs1143627), IL-6 (IL-6; rs1800795), tumor necrosis factor-α (TNF-α; rs1800629), and resistin (RETN; rs1862513, rs3219177, rs3745367, rs3745368). Biochemical analysis included determination of circulating adipokines, C-reactive protein (CRP) levels, lipid profile, and markers of insulin resistance.

RESULTS

Compared to males, females presented higher circulating levels of insulin, adiponectin, IL-6, resistin, and leptin concentrations, but lower TNF-α levels. No statistically significant differences were found for genotype or allelic distributions between genders. In the whole sample population, adiponectin levels were influenced by ADIPOQ rs17300539 (c.-1138G>A; lower in subjects with GG genotype). When only males were considered, IL-1β, IL-6, and TNF-α levels were associated with ADIPOQ rs1501299 (c.214 + 62G>T; higher in GG subjects). TNF-α concentrations were modulated by TNF-α rs1800629 (c.-488G>A; lower in GG males), RETN rs1862513 (c.-216C>G; higher in CC subjects), and RETN rs3219177 (c.118 + 39C>T; higher in CC subjects). Leptin levels were influenced by IL-1β rs1143627 (c.-118C>T) presenting TT individuals' lower levels.

CONCLUSIONS

Our data demonstrate that in pediatric obese patients, some adipokine gene SNPs have an association with circulating adipokine levels and lipid profile.

Genetic variants in genes of the inflammatory response in association with infective endocarditis

Aims

Inflammation in infective endocarditis (IE) is a complex network including interactions of inflammatory cytokines and other components of host response. Certainly, any variation in this network could influence susceptibility or disease progression of IE. In this study, 14 single nucleotide variants (SNVs) in genes coding for interleukin-1β, interleukin-6, interleukin-10, toll–like receptor-4, tumor necrosis factor-α, selectin E and intercellular adhesion molecule-1 were analyzed for an association with susceptibility to IE and correlated with disease-related laboratory parameters. Furthermore, the occurrence of SNVs was examined to elucidate pathogen-dependent associations.

Methods and Results

The distribution of SNVs was determined in IE-patients and healthy blood donors by RFLP analysis. White blood cells (WBC) were counted using flow cytometry, concentration of C-reactive protein and procalcitonin was measured immunologically. Interleukin-6 c.471+870G>A genotypes differed significantly between IE patients and controls. The frequency of the heterozygote genotype GA was considerably higher in the patient group (68.9% vs. 43.8%, P_c<0.0003). Interleukin-6 c.-237 minor allele frequency was increased in patients, although not statistically significant. Additionally, we detected a potential relation between interleukin-1β c.315C>T and IE. Pathogen-dependent analysis showed no significantly associated subgroup in relation to IE susceptibility, but gave hints towards alterations regarding Enterococcus-caused IE cases. Patients with genotype selectin-E c.-19 GT tend to have higher preoperative WBC counts than patients with genotype GG. We further showed an association between two interleukin-1β SNVs and laboratory biomarkers.

Conclusion

This study shows genetic predispositions for the establishment of IE. Furthermore, correlation of SNVs with disease-related biomarkers suggests a role of genetic variants regarding the inflammatory response in IE.

Interleukin-1 beta polymorphisms are associated with lymph node metastasis in Korean patients with papillary thyroid carcinoma

In this study, we investigated whether single nucleotide polymorphisms (SNPs) of the interleukin-1 beta (IL-1B) were associated with papillary thyroid carcinoma (PTC). We also assessed the relationships between IL-1B SNPs and the clinicopathologic characteristics of PTC patients. Ninety-three PTC patients and 324 controls were recruited. The patients with PTC were dichotomized and compared with respect to the clinicopathologic characteristics of PTC. Seven SNPs in the IL-1B gene were selected and genotyped using direct sequencing. Four SNPs (rs1143627, rs3136558, rs1143633, and rs1143643) in the IL-1B gene were significantly associated with PTC (p < 0.05). In clinicopathologic features, 3 SNPs (rs1143630, rs1143633, and rs1143643) showed a strong relationship with lymph node metastasis of PTC. The genotype and allele frequencies of rs1143630 and rs1143643 remained significantly associated with lymph node metastasis after Bonferroni correction for multiple testing. In haplotype analysis, two linkage disequilibrium blocks (block 1 consisted of rs1143627, rs3917356, and rs1143630; block 2 consisted of rs1143633 and rs1143643) also revealed significant associations with lymph node metastasis. Our results suggest that IL-1B polymorphisms may be associated with the risk of PTC in the Korean population. Especially, IL-1B polymorphisms might be a predictive factor for lymph node metastasis of PTC patients.

Functional analysis of a lung cancer risk haplotype in the IL1B gene regulatory region

Interleukin-1β (IL-1β), encoded by the IL1B gene, is a cytokine important in regulation of the inflammatory response. Elevated levels of IL1B expression have been associated with risk of gastric and lung cancer. We previously reported that a certain haplotype containing four single-nucleotide polymorphisms (SNPs) (-3893G, -1464G, -511C and -31T; GGCT) in the IL1B gene regulatory region was associated with lung cancer risk and increased expression of the IL1B gene in the lung. In the present study, we have cloned the two haplotypes that were either protective (ACTC) or increasing lung cancer risk (GGCT) in a luciferase reporter vector system. We also cloned the IL1B -3893 and -1464 SNPs that were found to be associated with risk of lung cancer. The haplotype associated with lung cancer risk showed higher transcriptional activity in the human lung epithelial A549 cell line in vitro. We also found that the IL1B -1464C allele increased transcriptional activity compared with the -1464G allele in the tumor necrosis factor α-stimulated cells, as well as specific transcription factor binding patterns to the IL1B -1464C allele. Interestingly, in vitro results showed a similar expression pattern as observed in the normal lung tissues of lung cancer patients reported earlier.

Cardiovascular genomics: a biomarker identification pipeline

Genomic biomarkers are essential for understanding the underlying molecular basis of human diseases such as cardiovascular disease. In this review, we describe a biomarker identification pipeline for cardiovascular disease, which includes 1) high-throughput genomic data acquisition, 2) preprocessing and normalization of data, 3) exploratory analysis, 4) feature selection, 5) classification, and 6) interpretation and validation of candidate biomarkers. We review each step in the pipeline, presenting current and widely used bioinformatics methods. Furthermore, we analyze several publicly available cardiovascular genomics datasets to illustrate the pipeline. Finally, we summarize the current challenges and opportunities for further research.

Genetic contribution to C-reactive protein levels in severe obesity

Obese individuals are characterized by a chronic, low-grade inflammatory state. Increased levels of C-reactive protein (CRP), a marker of inflammation, have been observed in subjects with the metabolic syndrome. We have previously reported that genes encoding proteins involved in the anti-inflammatory and immune response are differentially expressed in visceral adipose tissue of obese men with or without the metabolic syndrome. Among these genes, the interferon-gamma-inducible protein 30 (IFI30), CD163 molecule (CD163), chemokine (C-X-C motif) ligand 9 (CXCL9) and thymic stromal lymphopoietin (TSLP), were selected for further genetic analyses. The aim of the study was to verify whether IFI30, CD163, CXCL9 and TSLP gene polymorphisms contribute to explain the inter-individual variability of the inflammatory profile of obesity assessed by plasma high-sensitivity CRP concentrations. A total of 1185 severely obese individuals were genotyped for single nucleotide polymorphisms (SNPs) covering most of the sequence-derived genetic variability at the IFI30, CD163, CXCL9 and TSLP gene loci (total of 27 SNPs). Following measurement of plasma CRP levels, subjects were divided into two groups, low vs. high using the median value of plasma CRP levels (8.31 mg/L) as a cutoff point. Genotype frequencies were compared between groups. Associations between genotypes and plasma CRP levels (continuous variable) were also tested after adjustments for age, sex, smoking and BMI. The rs11554159 and rs7125 IFI30 SNPs showed a significant difference in genotype frequencies (p<0.05) between subgroups of low vs. high plasma CRP levels (wild type homozygotes: rs11554159=47% vs. 55%, rs7125=31% vs. 24%, for low vs. high CRP groups, respectively). The association between rs11554159 and CRP levels as a continuous variable remained significant (p=0.004). Both carriers of the GA and AA genotypes demonstrated, on average, a 13% lower CRP levels in comparison with GG homozygotes. No association was observed between SNPs in the CD163, CXCL9 and TSLP genes and CRP levels. The IFI30 rs11554159 polymorphism could partially explain the inter-individual variability observed in the inflammatory profile associated with obesity.

Fatigued breast cancer survivors and gene polymorphisms in the inflammatory pathway

Chronic fatigue (CF) in breast cancer survivors (BCSs) has been associated with increased serum C-reactive protein-levels (CRP), pro-inflammatory cytokines and cytokine gene single nucleotide polymorphisms (SNPs). Still, there are few studies on these topics, and due to small study-cohorts the possibility to adjust for other conditions related to inflammatory processes, e.g. depression, has been limited. In 302 BCSs, examined approximately four years after treatment for breast cancer stage II/III, data on high sensitivity (hs)CRP, leukocytes and mRNA interleukin (IL)1β and IL6R expression, depression and chronic fatigue were available. Three years thereafter, 236 BCSs were re-examined. The associations between fatigue and SNPs in inflammation-related genes; IL1β (rs16944), IL6 (rs1800795), IL6receptor (rs4129267, rs4845617, rs2228145), CRP (rs2794521, rs3091244) were investigated, together with the relations between SNPs in IL6R,IL1β and CRP genes and mRNA blood expression levels of IL6R and IL1β and serum hsCRP-levels, respectively. All analyses were repeated after exclusion of depressed individuals and separating BCSs with persistent fatigue from never-fatigued individuals. Even after exclusion of depressed individuals neither the SNPs nor the mRNA IL1β and IL6R expression levels were associated with chronic or persistent fatigue. In the subset of persistent fatigued and never-fatigued individuals the CRP SNP (rs3091244) was associated with hsCRP level (p=0.02). IL1β and IL6R mRNA expression levels were not related to the IL1β and IL6R genotypes. In a large cohort of BCSs the investigated SNPs in inflammation-related genes were not associated with fatigue, though subset analyses indicated an association between the CRP SNP (rs3091244) and serum hsCRP.

Genetic variation of the interleukin-1 family and nongenetic factors determining the interleukin-1 receptor antagonist phenotypes

The natural anti-inflammatory protein interleukin-1 receptor antagonist (IL-1Ra) inhibits the activity of IL-1 and is associated with vascular injury and metabolic disorders. We analyzed genetic and nongenetic determinants of the IL-1Ra phenotype. Fifteen haplotype-tagging single nucleotide polymorphisms (SNPs) in the IL-1α (IL1A), IL-1β (IL1B), and IL-1 receptor antagonist (IL-1RN) genes were determined in the Health 2000 survey (n = 6771) and European myocardial infarction (MI) survivors (n = 972). Three SNPs were genotyped in the FINRISK97 (FR97) study (n = 7222). We found 3 IL1RN variants that were associated with the IL-1Ra phenotype in the study populations and remained significant after Bonferroni correction with increasing significance in meta-analysis (P values for rs3213448,rs315952, rs315949, respectively: 5.5 x 10(-11), 1.5 x 10(-11), and 4.0 x 10(-14)). Minor allele of the rare IL1B variant rs1143642 was associated with decreased IL-1Ra levels in the Health 2000 and FR97 populations, and the association strengthened in the meta-analysis (P = 9.4 x 10(-7)). The proportion of variance explained by the IL1RN variant was larger in MI survivors (5.0%) than in the unselected population (0.5%). Body mass index was the strongest nongenetic predictor of the IL-1Ra phenotype, explaining 11.8% of the variance in Health 2000, 18.1% in FR97, and 25% in MI survivors. In conclusion, 3 IL1RN SNPs and 1 IL1B variant were determining IL-1Ra phenotype independently of body mass index and other metabolic phenotypes. The proportion of phenotypic variation in IL-1Ra explained by the genetic variants was, however, modest compared with the proportion explained by the body mass index.

Interleukin-1 cluster gene polymorphisms in childhood IgA nephropathy

We have carried out a study with the aim of investigating the association between single nucleotide polymorphisms (SNPs) of the IL-1 gene cluster and childhood IgA nephropathy (IgAN). SNPs of the IL-1 alpha, IL-1 beta, and IL-1 receptor antagonist (RN) genes (IL1A, IL1B, and IL1RN, respectively) were analyzed in 182 patients with childhood IgAN and in 500 healthy controls. The IgAN patients were also dichotomized and compared with respect to proteinuria (<4 mg and >or=4 mg/m(2) per hour, respectively), the presence or absence of podocyte foot process effacement, and the presence of pathologically early and advanced disease markers, such as interstitial fibrosis, tubular atrophy, or global sclerosis. Significant differences in SNP frequencies were observed for the IL1B and IL1RN genes (rs1143627, rs3917356, and rs1143633 in the IL1B gene, and rs928940, rs439154, and rs315951 in the IL1RN gene). Moreover, rs1143627, rs3917356, and rs1143633 of IL1B were found to be significantly associated with the presence of podocyte foot process effacement. Our results suggest that the IL1B and IL1RN genes are associated with increased susceptibility to IgAN in children. They also suggest that the development of proteinuria in IgAN is related to IL1A and that podocyte foot process effacement is associated with IL1B.