Reduced ech-6 expression attenuates fat-induced lifespan shortening in C. elegans

Deregulated energy homeostasis represents a hallmark of aging and results from complex gene-by-environment interactions. Here, we discovered that reducing the expression of the gene ech-6 encoding enoyl-CoA hydratase remitted fat diet-induced deleterious effects on lifespan in Caenorhabditis elegans, while a basal expression of ech-6 was important for survival under normal dietary conditions. Lipidomics revealed that supplementation of fat in ech-6-silenced worms had marginal effects on lipid profiles, suggesting an alternative fat utilization for energy production. Transcriptomics further suggest a causal relation between the lysosomal pathway, energy production, and the longevity effect conferred by the interaction between ech-6 and fat diets. Indeed, enhancing energy production from endogenous fat by overexpressing lysosomal lipase lipl-4 recapitulated the lifespan effects of fat diets on ech-6-silenced worms. Collectively, these results suggest that the gene ech-6 is potential modulator of metabolic flexibility and may be a target for promoting metabolic health and longevity.

Multiplexing protein and gene level measurements on a single Luminex platform

BACKGROUND

The ability to simultaneously measure multiple secreted proteins and the corresponding gene expression levels from a single sample is valuable for comprehensive analysis. Bottlenecks to traditional immunoassays and gene expression assays include large sample consumption, time consuming experimental procedures, and complex data analysis.

METHOD AND RESULTS

Here, we demonstrate two high-throughput assays measuring both messenger RNA (mRNA) expression and proteins in a single sample run on a Luminex platform. Human peripheral blood mononuclear cells (hPBMCs) were treated with lipopolysaccharide (LPS) and harvested at 24 and 72 h. Samples were assayed with the ProcartaPlex Human Immune Monitoring 65-plex Panel for protein and corresponding mRNA targets on a QuantiGene Human 80-plex Panel.

CONCLUSION

Multiplexing ProcartaPlex and QuantiGene Plex assays provide a broad survey of protein levels and gene expression networks.

Metabolomics in the clinic: A review of the shared and unique features of untargeted metabolomics for clinical research and clinical testing

Metabolomics is the untargeted measurement of the metabolome, which is composed of the complement of small molecules detected in a biological sample. As such, metabolomic analysis produces a global biochemical phenotype. It is a technology that has been utilized in the research setting for over a decade. The metabolome is directly linked to and is influenced by genetics, epigenetics, environmental factors, and the microbiome-all of which affect health. Metabolomics can be applied to human clinical diagnostics and to other fields such as veterinary medicine, nutrition, exercise, physiology, agriculture/plant biochemistry, and toxicology. Applications of metabolomics in clinical testing are emerging, but several aspects of its use as a clinical test differ from applications focused on research or biomarker discovery and need to be considered for metabolomics clinical test data to have optimum impact, be meaningful, and be used responsibly. In this review, we deconstruct aspects and challenges of metabolomics for clinical testing by illustrating the significance of test design, accurate and precise data acquisition, quality control, data processing, n-of-1 comparison to a reference population, and biochemical pathway analysis. We describe how metabolomics technology is integral to defining individual biochemical phenotypes, elaborates on human health and disease, and fits within the precision medicine landscape. Finally, we conclude by outlining some future steps needed to bring metabolomics into the clinical space and to be recognized by the broader medical and regulatory fields.

Associations of LBX1 gene and adolescent idiopathic scoliosis susceptibility: a meta-analysis based on 34,626 subjects

Background

The results of studies investigating the association between the ladybird homeobox 1 (LBX1) gene polymorphisms and the risk of adolescent idiopathic scoliosis (AIS) are not all the same. As such, we performed a meta-analysis to estimate the association between LBX1 gene polymorphisms and AIS susceptibility.

Methods

Relevant studies published before 15 November 2015 were identified by searching PubMed, EMBASE, ISI web of knowledge, EBSCO, CNKI and CBM. The strength of relationship was assessed by using odds ratios (ORs) and 95 % confidence interval (CI).

Results

A total number of eight case-control studies including 10,088 cases and 24,538 controls were identified. The results showed that T allele of rs111090870 increased AIS susceptibility in Asians (T vs. C, OR = 1.22, 95 % CI: 1.16–1.29, P < 0.001), Caucasians (T vs. C, OR = 1.17, 95 % CI: 1.14–1.21, P < 0.001) and in female (T vs. C, OR = 1.21, 95 % CI: 1.17–1.25, P < 0.001). The G allele of rs678741 decreased AIS risk in female (G vs. A, OR = 0.83, 95 % CI: 0.81–0.85, P < 0.001), and the G allele of the rs625039 increased AIS susceptibility in Asians (G vs. A, OR = 1.14, 95 % CI: 1.11–1.17, P < 0.001).

Conclusions

Our meta-analysis provides evidence that rs111090870, rs678741 and rs625039 polymorphisms near LBX1 gene are associated with AIS susceptibility in some populations. However, our findings are based on only a limited number of studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12891-016-1139-z) contains supplementary material, which is available to authorized users.

Systems proteomics of liver mitochondria function

Recent improvements in quantitative proteomics approaches, including Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS), permit reproducible large-scale protein measurements across diverse cohorts. Together with genomics, transcriptomics, and other technologies, transomic data sets can be generated that permit detailed analyses across broad molecular interaction networks. Here, we examine mitochondrial links to liver metabolism through the genome, transcriptome, proteome, and metabolome of 386 individuals in the BXD mouse reference population. Several links were validated between genetic variants toward transcripts, proteins, metabolites, and phenotypes. Among these, sequence variants in Cox7a2l alter its protein's activity, which in turn leads to downstream differences in mitochondrial supercomplex formation. This data set demonstrates that the proteome can now be quantified comprehensively, serving as a key complement to transcriptomics, genomics, and metabolomics--a combination moving us forward in complex trait analysis.

The Convergence of Systems and Reductionist Approaches in Complex Trait Analysis

Research into the genetic and environmental factors behind complex trait variation has traditionally been segregated into distinct scientific camps. The reductionist approach aims to decrypt phenotypic variability bit by bit, founded on the underlying hypothesis that genome-to-phenome relations are largely constructed from the additive effects of their molecular players. In contrast, the systems approach aims to examine large-scale interactions of many components simultaneously, on the premise that interactions in gene networks can be both linear and non-linear. Both approaches are complementary, and they are becoming increasingly intertwined due to developments in gene editing tools, omics technologies, and population resources. Together, these strategies are beginning to drive the next era in complex trait research, paving the way to improve agriculture and toward more personalized medicine.

Association of the glucokinase gene promoter polymorphism -30G > A (rs1799884) with gestational diabetes mellitus susceptibility: a case-control study and meta-analysis

PURPOSE

Several studies have examined the association between glucokinase (GCK)-30G > A polymorphism and gestational diabetes mellitus (GDM). However, the results are still controversial. We performed the case-control study to investigate whether GCK-30G > A polymorphism correlates with the susceptibility of GDM in Chinese populations, and then conducted a meta-analysis by combining the previous studies.

METHODS

We recruited 948 GDM patients and 975 controls from May 2011 to August 2013. All the subjects were genotyped using the PCR-based invader assay. The differences of allelic frequencies and genotype distributions between GDM patients and controls were investigated in case-control study. A systematic search of all relevant studies was conducted. The observational studies that were related to an association between the glucokinase (GCK)-30G > A polymorphism and GDM were identified. The association between the glucokinase (GCK)-30G > A polymorphism and GDM susceptibility was assessed using genetic models.

RESULTS

The case-control study showed that GCK-30G > A polymorphism was associated with the susceptibility of GDM in a Chinese population. Furthermore, other six previously reported studies were included to perform meta-analysis. The meta-analysis showed that GCK-30G > A polymorphism was associated with GDM in Caucasian and Asian.

CONCLUSIONS

This study suggested that GCK-30G > A polymorphism may be associated with the susceptibility of GDM in a Chinese population. The further meta-analysis provides additional evidence supporting the above result that the risk allele of the GCK-30G > A polymorphism may increase GDM risk.

Association between single nucleotide polymorphism of IL15RA gene with susceptibility to ossification of the posterior longitudinal ligament of the spine

Background

Previous studies reported the association between single nucleotide polymorphism (SNP) of IL15 receptor alpha (IL15RA) gene with susceptibility to ossification of the posterior longitudinal ligament of the spine (OPLL). However, the results were still in controversy. Therefore, the purpose of the present study was to investigate the association between SNPs of IL15RA gene with susceptibility to OPLL in a Chinese Han population.

Methods

A total of 235 OPLL patients and 250 age-matched healthy controls were recruited. All the subjects were genotyped using the PCR (polymerase chain reaction)-based invader assay. A case–control study was performed to define the contribution of rs2228059 and rs2296139 to predisposition of OPLL. We also performed subgroup analysis according to the different gender.

Results

A significant association of rs2228059 with OPLL was observed in the Chinese Han population (p <0.001, OR = 1.63, 95% CI = 1.26–2.11). The subgroup analysis showed that there was a significant association between the allele frequency of rs2228059 and the susceptibility of OPLL in males (p = 0.002, OR = 1.72, 95% CI = 1.23–2.42). However, there was no significant association between SNP of rs2296139 and susceptibility to OPLL.

Conclusions

The present study demonstrates that the SNP of rs2228059 in IL15RA gene is associated with susceptibility to OPLL in a Chinese Han population, especially in males.

Association Between rs11190870 Polymorphism Near LBX1 and Susceptibility to Adolescent Idiopathic Scoliosis in East Asian Population: A Genetic Meta-Analysis

STUDY DESIGN

Meta-analysis to collect all the relevant studies to date to further investigate whether or not the rs11190870 polymorphism is associated with susceptibility to adolescent idiopathic scoliosis (AIS) in East Asian population.

OBJECTIVE

To investigate whether or not the rs11190870 polymorphism is associated with susceptibility to AIS in East Asian population.

SUMMARY OF BACKGROUND DATA

To date, the single nucleotide polymorphism rs11190870 was identified as the most significant common variant in Japanese females. Three association studies conducted in Chinese Han population from Hong Kong, Yangtze River region, and Southern region of mainland China replicated the association between AIS and rs1190870. However, there is limited published data about the association of rs11190870 with AIS in East Asian population.

METHODS

A systematic search of all relevant studies published through August 2013 was conducted using the MEDLINE, EMBASE, OVID, and ScienceDirect. Single nucleotide polymorphism of rs11190870 was evaluated. The included studies were assessed in the analysis of the following allele model: T allele versus C allele for the allele-level comparison; (b) TC + TT versus CC for dominant model of T allele; (c) TT versus TC + CC for recessive model of T allele, and (d) TT versus CC for extreme genotype.

RESULTS

Four studies with 8415 total participants (2889 patients with AIS and 5526 controls), who were all East Asian population, were eligible for inclusion. We searched for genotypes T allele versus C allele, TT versus TC + CC, TC + TT versus CC, and TT versus CC in a fixed/random-effects model. The effect summary odds ratios and 95 % confidence intervals were obtained, which shows significant association between rs11190870 and AIS in East Asian populations (all genetic models P < 0.001). Subgroup analyses were conducted according to sex. The results showed a significant association between rs11190870 and AIS in female (all genetic models, P < 0.001) but not in male (all genetic models, P > 0.05).

CONCLUSION

The present meta-analysis demonstrated that the T allele of single nucleotide polymorphism rs11190870 may be a major susceptibility locus in the East Asian population with AIS, especially in female.

LEVEL OF EVIDENCE

1.

Lack of association between the CHL1 gene and adolescent idiopathic scoliosis susceptibility in Han Chinese: a case-control study

Background

A previous genome-wide association study (GWAS) suggested a strong association between the single nucleotide polymorphism (SNP) rs10510181 in the proximity of the gene encoding a cell adhesion molecule with homology to L1CAM (CHL1) and adolescent idiopathic scoliosis (AIS) in Caucasians. To clarify the role of CHL1 in the etiopathogenesis of AIS, we performed a case-control replication study in a Han Chinese population.

Methods

Five hundred female AIS patients between 10 and 18 years of age, as well as 500 age- and sex-matched controls were included. This study was conducted as a 2-stage case-control analysis: initial screening for the association between AIS and SNPs in and around the CHL1 gene (186 cases and 169 controls) followed by a confirmation test (314 cases and 331 controls). rs10510181 and 4 SNPs (rs2055314, rs331894, rs2272522, and rs2272524) in the CHL1 gene were selected for genotyping.

Results

Putative associations were shown between AIS and rs10510181, rs2055314, and rs2272522 in stage I. However, the associations were not confirmed in stage II. For rs10510181, the genotype frequencies were GG 28.8%, GA 46.2%, and AA 25.0% in AIS patients and GG 29.8%, GA 48.8%, and AA 21.4% in controls. No significant difference was found in genotype distribution between cases and controls (P = 0.39). Similarly, the genotype and allele distribution were comparable between case and control for rs2055314 and rs2272522.

Conclusions

There was no statistical association between polymorphisms of the CHL1 gene and idiopathic scoliosis in a Chinese population.

To control false positives in gene-gene interaction analysis: two novel conditional entropy-based approaches

Genome-wide analysis of gene-gene interactions has been recognized as a powerful avenue to identify the missing genetic components that can not be detected by using current single-point association analysis. Recently, several model-free methods (e.g. the commonly used information based metrics and several logistic regression-based metrics) were developed for detecting non-linear dependence between genetic loci, but they are potentially at the risk of inflated false positive error, in particular when the main effects at one or both loci are salient. In this study, we proposed two conditional entropy-based metrics to challenge this limitation. Extensive simulations demonstrated that the two proposed metrics, provided the disease is rare, could maintain consistently correct false positive rate. In the scenarios for a common disease, our proposed metrics achieved better or comparable control of false positive error, compared to four previously proposed model-free metrics. In terms of power, our methods outperformed several competing metrics in a range of common disease models. Furthermore, in real data analyses, both metrics succeeded in detecting interactions and were competitive with the originally reported results or the logistic regression approaches. In conclusion, the proposed conditional entropy-based metrics are promising as alternatives to current model-based approaches for detecting genuine epistatic effects.

Addressing the Challenges of Detecting Epistasis in Genome-Wide Association Studies of Common Human Diseases Using Biological Expert Knowledge

Recent technological developments in the field of genetics have given rise to an abundance of research tools, such as genome-wide genotyping, that allow researchers to conduct genome-wide association studies (GWAS) for detecting genetic variants that confer increased or decreased susceptibility to disease. However, discovering epistatic, or gene-gene, interactions in high dimensional datasets is a problem due to the computational complexity that results from the analysis of all possible combinations of single-nucleotide polymorphisms (SNPs). A recently explored approach to this problem employs biological expert knowledge, such as pathway or protein-protein interaction information, to guide an analysis by the selection or weighting of SNPs based on this knowledge. Narrowing the evaluation to gene combinations that have been shown to interact experimentally provides a biologically concise reason why those two genes may be detected together statistically. This chapter discusses the challenges of discovering epistatic interactions in GWAS and how biological expert knowledge can be used to facilitate genome-wide genetic studies.

Association of rs11190870 near LBX1 with adolescent idiopathic scoliosis susceptibility in a Han Chinese population

PURPOSE

To investigate whether rs11190870 near LBX1 correlates with the susceptibility or curve progression of adolescent idiopathic scoliosis (AIS) in a Han Chinese population.

METHODS

A total of 949 AIS patients and 976 age-matched healthy controls were recruited. All the subjects were genotyped using the PCR-based invader assay. Case-control study and case-only study were performed to define the contribution of rs11190870 to predisposition and curve severity of AIS. Additionally, we further conducted a meta-analysis of the study findings together with those of previously reported studies.

RESULTS

A significant association of rs11190870 with AIS was observed in the Han Chinese population (P = 1.8 × 10(-9); odd ratio = 1.51; 95 % confidence interval = 1.33-1.71), and AIS patients with TT genotype had a larger Cobb angle than those with TC or CC genotype (P = 0.005). The meta-analysis confirmed that the positive association of this SNP with AIS in the East Asian population.

CONCLUSIONS

The SNP rs11190870 near LBX1 is associated with both susceptibility and curve progression of AIS.

Role for protein-protein interaction databases in human genetics

Proteomics and the study of protein-protein interactions are becoming increasingly important in our effort to understand human diseases on a system-wide level. Thanks to the development and curation of protein-interaction databases, up-to-date information on these interaction networks is accessible and publicly available to the scientific community. As our knowledge of protein-protein interactions increases, it is important to give thought to the different ways that these resources can impact biomedical research. In this article, we highlight the importance of protein-protein interactions in human genetics and genetic epidemiology. Since protein-protein interactions demonstrate one of the strongest functional relationships between genes, combining genomic data with available proteomic data may provide us with a more in-depth understanding of common human diseases. In this review, we will discuss some of the fundamentals of protein interactions, the databases that are publicly available and how information from these databases can be used to facilitate genome-wide genetic studies.

Introduction to omics

Exploiting the potential of omics for clinical diagnosis, prognosis, and therapeutic purposes has currently been receiving a lot of attention. In recent years, most of the effort has been put into demonstrating the possible clinical applications of the various omics fields. The cost-effectiveness analysis has been, so far, rather neglected. The cost of omics-derived applications is still very high, but future technological improvements are likely to overcome this problem. In this chapter, we will give a general background of the main omics fields and try to provide some examples of the most successful applications of omics that might be used in clinical diagnosis and in a therapeutic context.

Review. Genetics of addictions: strategies for addressing heterogeneity and polygenicity of substance use disorders

Addictions are common psychiatric disorders that exert high cost to the individual and to society. Addictions are a result of the interplay of multiple genetic and environmental factors. They are characterized by phenotypic and genetic heterogeneity as well as polygenicity, implying a contribution of different neurobiological mechanisms to the clinical diagnosis. Therefore, treatments for most substance use disorders are often only partially effective, with a substantial proportion of patients failing to respond. To address heterogeneity and polygenicity, strategies have been developed to identify more homogeneous subgroups of patients and to characterize genes contributing to their phenotype. These include genetic linkage and association studies as well as functional genetic analysis using endophenotypes and animal behavioural experimentation. Applying these strategies in a translational context aims at improving therapeutic response by the identification of subgroups of addiction patients for individualized, targeted treatment strategies. This article aims to discuss strategies addressing heterogeneity and polygenicity of substance use disorders by presenting results of recent research on genetic and environmental components of addiction. It will also introduce the European IMAGEN study that aims to integrate methodical approaches discussed in order to identify the genetic and neurobiological basis of behavioural traits relevant to the development of addictions.

From human genetics and genomics to pharmacogenetics and pharmacogenomics: past lessons, future directions

A brief history of human genetics and genomics is provided, comparing recent progress in those fields with that in pharmacogenetics and pharmacogenomics, which are subsets of genetics and genomics, respectively. Sequencing of the entire human genome, the mapping of common haplotypes of single-nucleotide polymorphisms (SNPs), and cost-effective genotyping technologies leading to genome-wide association (GWA) studies - have combined convincingly in the past several years to demonstrate the requirements needed to separate true associations from the plethora of false positives. While research in human genetics has moved from monogenic to oligogenic to complex diseases, its pharmacogenetics branch has followed, usually a few years behind. The continuous discoveries, even today, of new surprises about our genome cause us to question reviews declaring that "personalized medicine is almost here" or that "individualized drug therapy will soon be a reality." As summarized herein, numerous reasons exist to show that an "unequivocal genotype" or even an "unequivocal phenotype" is virtually impossible to achieve in current limited-size studies of human populations. This problem (of insufficiently stringent criteria) leads to a decrease in statistical power and, consequently, equivocal interpretation of most genotype-phenotype association studies. It remains unclear whether personalized medicine or individualized drug therapy will ever be achievable by means of DNA testing alone.