Association of common variants in JAK2 gene with reduced risk of metabolic syndrome and related disorders

Mediation effect of JAK2 methylation on the association between sitting time and abdominal obesity in rural adults

BACKGROUND

Sitting time may affect health by altering the methylation of certain genes. This research aimed to estimate the association of sitting time with abdominal obesity and the role of Janus kinase 2 (JAK2) methylation in the association among rural adults.

METHODS

A total of 1062 rural adults from the Henan Rural Cohort Study were included. Whole blood was used to extract genomic DNA. JAK2 DNA methylation level was assessed by MethylTargetTM. The logistic regression model was utilized to assess the association of sitting time with abdominal obesity, and the possible effect of JAK2 DNA methylation on the association were conducted by using mediation analyses.

RESULTS

Average time of sitting of participants was 7.28 ± 3.37 h/d. For per 1 h increment in sitting time, the odd ratio (OR) and 95% confidence interval (CI) of abdominal obesity was 1.153 (1.095, 1.214) after controlling potential risk factors. Simultaneously, the methylation levels of Chr9: 4985407 site and Chr9: 4985238-4985455 region were negatively correlated with abdominal obesity (OR: 0.549, 95% CI: 0.394, 0.765; OR: 0.189, 95% CI: 0.056, 0.640, respectively). Moreover, Chr9: 4985407 site and Chr9: 4985238-4985455 region methylation levels mediated the association of sitting time with abdominal obesity, and the indirect effects account for 6.78% and 4.24%, respectively.

CONCLUSIONS

Longer sitting time was positively correlated with abdominal obesity in the rural population, and methylation level of JAK2 may be an underlying mediation of the effect.

Modelling porcine NAFLD by deletion of leptin and defining the role of AMPK in hepatic fibrosis

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is the most prevalent cause of chronic hepatic disease and results in non-alcoholic steatohepatitis (NASH), which progresses to fibrosis and cirrhosis. Although the Leptin deficient rodent models are widely used in study of metabolic syndrome and obesity, they fail to develop liver injuries as in patients.

METHODS

Due to the high similarity with humans, we generated Leptin-deficient (Leptin-/-) pigs to investigate the mechanisms and clinical trials of obesity and NAFLD caused by Leptin.

RESULTS

The Leptin-/- pigs showed increased body fat and significant insulin resistance at the age of 12 months. Moreover, Leptin-/- pig developed fatty liver, non-alcoholic steatohepatitis and hepatic fibrosis with age. Absence of Leptin in pig reduced the phosphorylation of JAK2-STAT3 and AMPK. The inactivation of JAK2-STAT3 and AMPK enhanced fatty acid β-oxidation and leaded to mitochondrial autophagy respectively, and both contributed to increased oxidative stress in liver cells. In contrast with Leptin-/- pig, although Leptin deletion in rat liver inhibited JAK2-STAT3 phosphorylation, the activation of AMPK pathway might prevent liver injury. Therefore, β-oxidation, mitochondrial autophagy and hepatic fibrosis did not occurred in Leptin-/- rat livers.

CONCLUSIONS

The Leptin-deficient pigs presents an ideal model to illustrate the full spectrum of human NAFLD. The activity of AMPK signaling pathway suggests a potential target to develop new strategy for the diagnosis and treatment of NAFLD.

Gene expression associations with body mass index in the Multi-Ethnic Study of Atherosclerosis

BACKGROUND/OBJECTIVES

Obesity, defined as excessive fat accumulation that represents a health risk, is increasing in adults and children, reaching global epidemic proportions. Body mass index (BMI) correlates with body fat and future health risk, yet differs in prediction by fat distribution, across populations and by age. Nonetheless, few genetic studies of BMI have been conducted in ancestrally diverse populations. Gene expression association with BMI was assessed in the Multi-Ethnic Study of Atherosclerosis (MESA) in four self-identified race and ethnicity (SIRE) groups to identify genes associated with obesity.

SUBJECTS/METHODS

RNA-sequencing was performed on 1096 MESA participants (37.8% white, 24.3% Hispanic, 28.4% African American, and 9.5% Chinese American) and linear models were used to assess the association of expression from each gene for its effect on BMI, adjusting for age, sex, sequencing center, study site, five expression and four genetic principal components in each self-identified race group. Sample-size-weighted meta-analysis was performed to identify genes with BMI-associated expression across ancestry groups.

RESULTS

Within individual SIRE groups, there were zero to three genes whose expression is significantly (p < 1.97 × 10^-6) associated with BMI. Across all groups, 45 genes were identified by meta-analysis whose expression was significantly associated with BMI, explaining 29.7% of BMI variation. The 45 genes are expressed in a variety of tissues and cell types and are enriched for obesity-related processes including erythrocyte function, oxygen binding and transport, and JAK-STAT signaling.

CONCLUSIONS

We have identified genes whose expression is significantly associated with obesity in a multi-ethnic cohort. We have identified novel genes associated with BMI as well as confirmed previously identified genes from earlier genetic analyses. These novel genes and their biological pathways represent new targets for understanding the biology of obesity as well as new therapeutic intervention to reduce obesity and improve global public health.

JAK1 rs310241 and JAK3 rs3008 Genotypes May Increase Susceptibility to Psoriasis: A Case Control Study

BACKGROUND

Janus kinases (JAKs) are a family of non-receptor protein tyrosine kinases that are expressed in a variety of tissues. Several JAK-controlled cytokine receptor pathways are incriminated in the initiation and progression of psoriasis. Genetic polymorphisms influencing JAK expression would be anticipated to have a great impact on disease activity.

OBJECTIVE

The aim of the study was to evaluate the association between JAK1 rs310241 and JAK3 rs3008 polymorphisms and the risk of developing psoriasis.

METHODS

Blood samples of 150 patients and 120 controls were screened for nucleotide polymorphisms in JAK1 rs310241 and JAK3 rs3008 genes by using polymerase chain reaction (PCR)-restriction fragment length polymorphism technique.

RESULTS

The GG genotype of the JAK1 rs310241 and JAK3 rs3008 genes was significantly associated with an increase in psoriasis risk (p = 0.000, OR = 7.7, 95% CI = 2.8-21.5; p = 0.003, OR = 3.3, 95% CI = 1.5-6.9, respectively). The G allele of both genes was also associated with psoriasis susceptibility (p = 0.000, OR = 2.0, 95% CI = 1.4-2.8; p = 0.002, OR = 1.7, 95% CI = 1.2-2.4, respectively).

CONCLUSION

The results indicate a possible association between JAK1 rs310241 and JAK3 rs3008 gene polymorphisms and susceptibility to psoriasis. These findings validate the importance of these molecules in psoriasis and may enable the identification of the individuals most susceptible to the disease.

Common genetic variation in obesity, lipid transfer genes and risk of Metabolic Syndrome: Results from IDEFICS/I.Family study and meta-analysis

As the prevalence of metabolic syndrome (MetS) in children and young adults is increasing, a better understanding of genetics that underlie MetS will provide critical insights into the origin of the disease. We examined associations of common genetic variants and repeated MetS score from early childhood to adolescence in a pan-European, prospective IDEFICS/I.Family cohort study with baseline survey and follow-up examinations after two and six years. We tested associations in 3067 children using a linear mixed model and confirmed the results with meta-analysis of identified SNPs. With a stringent Bonferroni adjustment for multiple comparisons we obtained significant associations(p < 1.4 × 10⁻⁴) for 5 SNPs, which were in high LD (r² > 0.85) in the 16q12.2 non-coding intronic chromosomal region of FTO gene with strongest association observed for rs8050136 (effect size(β) = 0.31, p_Wald = 1.52 × 10⁻⁵). We also observed a strong association of rs708272 in CETP with increased HDL (p = 5.63 × 10⁻⁴⁰) and decreased TRG (p = 9.60 × 10⁻⁵) levels. These findings along with meta-analysis advance etiologic understanding of childhood MetS, highlighting that genetic predisposition to MetS is largely driven by genes of obesity and lipid metabolism. Inclusion of the associated genetic variants in polygenic scores for MetS may prove to be fundamental for identifying children and subsequently adults of the high-risk group to allow earlier targeted interventions.

PNA Clamping in Nucleic Acid Amplification Protocols to Detect Single Nucleotide Mutations Related to Cancer

This review describes the application of peptide nucleic acids (PNAs) as clamps that prevent nucleic acid amplification of wild-type DNA so that DNA with mutations may be observed. These methods are useful to detect single-nucleotide polymorphisms (SNPs) in cases where there is a small amount of mutated DNA relative to the amount of normal (unmutated/wild-type) DNA. Detecting SNPs arising from mutated DNA can be useful to diagnose various genetic diseases, and is especially important in cancer diagnostics for early detection, proper diagnosis, and monitoring of disease progression. Most examples use PNA clamps to inhibit PCR amplification of wild-type DNA to identify the presence of mutated DNA associated with various types of cancer.

Metabolic Effects of JAK1/2 Inhibition in Patients with Myeloproliferative Neoplasms

Ruxolitinib is an FDA approved janus kinase (JAK)1/2 inhibitor used to treat myeloproliferative neoplasms (MPNs), including myelofibrosis and polycythemia vera. We aimed to determine the metabolic consequences of ruxolitinib treatment in patients with MPNs. We performed a retrospective single-center cohort study utilizing an electronic medical record based database of patients who began treatment with ruxolitinib for MPNs from January 2010 to March 2017. We also examined the effects of ruxolitinib on adipose tissue JAK/STAT signaling in a mouse model. 127 patients were identified, of which 69 had data available for weight, and at least one other parameter of interest before, and 72 weeks after starting ruxolitinib. Mean baseline weight was 73.9 ± 17.0 kg, and 78.54 ± 19.1 kg at 72 weeks (p < 0.001). 50% of patients gained >5% body weight. Baseline body mass index (BMI) was 25.8 ± 4.8 kg/m², and 27.5 ± 5.5 kg/m² at 72 weeks (p < 0.001). Patients treated with ruxolitinib had a higher systolic blood pressure, serum AST, and ALT at 72 weeks, compared with baseline (p = 0.03, p = 0.01, p = 0.04, respectively). In mice, ruxolitinib decreased basal and GH-stimulated STAT5 phosphorylation in adipose tissue. As pharmacological JAK1/2 inhibitors are being developed and used in clinical practice, it is important to understand their long-term metabolic consequences.

Expression of GHR and Downstream Signaling Genes in Human Adipose Tissue-Relation to Obesity and Weight Change

CONTEXT

GH is a strong regulator of metabolism. In obesity, both GH secretion and adipose tissue GHR gene expression are decreased. More detailed information on the regulation of GHR, STAT3/5, and downstream-regulated genes in human adipose tissue during diet-induced weight loss and weight gain is lacking.

OBJECTIVE

The aim of the present study was to investigate the gene expression patterns of GHR and the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway (JAK2, STAT3, STAT5A, and STAT5B) in human subcutaneous adipose tissue in relation to energy restriction and overfeeding.

DESIGN, PATIENTS, AND INTERVENTIONS

Tissue distribution was analyzed in a data set generated by RNA sequencing containing information on global expression in human tissues. Subcutaneous adipose tissue or adipocyte gene expression (measured by DNA microarrays) was investigated in the following settings: (i) individuals with obesity vs individuals with normal weight; (ii) energy restriction; and (iii) overfeeding.

RESULTS

GHR expression was decreased in subjects with obesity compared with subjects with normal weight (P < 0.001). It was increased in response to energy restriction and decreased in response to overfeeding (P = 0.015 and P = 0.030, respectively). STAT3 expression was increased in subjects with obesity (P < 0.001). It was decreased during energy restriction and increased during overfeeding (P = 0.004 and P = 0.006, respectively). STAT3-regulated genes showed an overall view of overexpression in obesity.

CONCLUSIONS

The results of the present study have shown that GHR, STAT3, and STAT3-regulated genes are dynamically, and reciprocally, regulated at the tissue level in response to energy restriction and overfeeding, suggesting that GH signaling is perturbed in obesity.

JAK/STAT - Emerging Players in Metabolism

The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway is crucial for transducing signals from a variety of metabolically relevant hormones and cytokines including growth hormone, leptin, erythropoietin, IL4, IL6 and IFNγ. A growing body of evidence suggests that this pathway is dysregulated in the context of obesity and metabolic disease. Recent development of animal models has been instrumental in identifying the role of JAK/STAT signaling in the peripheral metabolic organs including adipose, liver, muscle, pancreas, and the immune system. In this review we summarize current knowledge about the function of JAK/STAT proteins in the regulation of metabolism, and highlight new potential therapeutic targets for the treatment of obesity and diabetes.

PCR-Based Detection Methods for Single-Nucleotide Polymorphism or Mutation: Real-Time PCR and Its Substantial Contribution Toward Technological Refinement

Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses. PCR-based methods for SNP/mutation detection are broadly categorized into two types-(1) polymorphic or mutant allele-directed specific analysis using primers matched with substituted nucleotide or using oligonucleotides to block or clamp the nontargeted template, and (2) melting curve analysis, which is combined with the real-time PCR techniques using hydrolysis probes, hybridization probes, or double-stranded DNA-binding fluorescent dyes. Innovative and novel approaches as well as technical improvements have made SNP- or mutation-detection methods increasingly more sophisticated. These advances include DNA/RNA preparation and subsequent amplification steps, and miniaturization of PCR instruments such that testing may be performed with relative ease in clinical laboratories or as a point-of-care test in clinical settings.

Targeting cytokine signaling in autoimmunity: back to the future and beyond

Cytokines represent structurally diverse soluble factors with critical roles in normal immune function and the pathogenesis of autoimmunity. The emergence of many successful biological therapies targeting cytokines and cytokine receptors exemplifies the importance of cytokines in driving human autoimmune disease; unsurprisingly, there is no paucity of reviews on this subject. Nonetheless, many patients with autoimmune disease do not respond to biologicals, and cure remains an unmet goal. Thus, targeting the intracellular pathways employed by cytokines provides new therapeutic opportunities. A subset of cytokines utilizes the Janus kinase-signal transducer of activators of transcription (JAK-STAT) pathway as a mode of signal transduction. First generation JAK inhibitors (jakinibs) are used to treat rheumatologic disease, and second-generation jakinibs are being developed. Simultaneously, rapid advances are being made in our understanding of the genomic and epigenomic impact of cytokines. In this review, we will briefly review the role of JAK-STAT-dependent cytokines in immune-mediated disease, the current status of Jakinibs, and future possibilities for therapeutic intervention using genomic insights.

Modeling progressive non-alcoholic fatty liver disease in the laboratory mouse

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease in the world and its prevalence is rising. In the absence of disease progression, fatty liver poses minimal risk of detrimental health outcomes. However, advancement to non-alcoholic steatohepatitis (NASH) confers a markedly increased likelihood of developing severe liver pathologies, including fibrosis, cirrhosis, organ failure, and cancer. Although a substantial percentage of NAFLD patients develop NASH, the genetic and molecular mechanisms driving this progression are poorly understood, making it difficult to predict which patients will ultimately develop advanced liver disease. Deficiencies in mechanistic understanding preclude the identification of beneficial prognostic indicators and the development of effective therapies. Mouse models of progressive NAFLD serve as a complementary approach to the direct analysis of human patients. By providing an easily manipulated experimental system that can be rigorously controlled, they facilitate an improved understanding of disease development and progression. In this review, we discuss genetically- and chemically-induced models of NAFLD that progress to NASH, fibrosis, and liver cancer in the context of the major signaling pathways whose disruption has been implicated as a driving force for their development. Additionally, an overview of nutritional models of progressive NAFLD is provided.

Meta-analyses between 18 candidate genetic markers and overweight/obesity

Aims

The goal of our study is to investigate the associations between 18 candidate genetic markers and overweight/obesity.

Methods

A total of 72 eligible articles were retrieved from literature databases including PubMed, Embase, SpingerLink, Web of Science, Chinese National Knowledge Infrastructure (CNKI), and Wanfang. Meta-analyses of 18 genetic markers among 56,738 controls and 48,148 overweight/obese persons were done by Review Manager 5.0.

Results

Our results showed that SH2B1 rs7498665 polymorphism was significantly associated with the risk of overweight/obesity (overall odds ratio (OR) = 1.21, 95% confidence interval (CI) = 1.09-1.34, P = 0.0004). Increased risk of overweight/obesity was also observed in FAIM2 rs7138803 polymorphism (overall OR = 1.11, 95% CI = 1.01-1.22, P = 0.04).

Conclusion

Our meta-analyses have shown the important role of 2 polymorphisms (SH2B1 rs7498665 and FAIM2 rs7138803) in the development of overweight/obesity. This study highlighted the importance of above two candidate genes (SH2B1 and FAIM2) in the risk of overweight/obesity.

Virtual slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2785487401176182.

Incorporating prior knowledge to increase the power of genome-wide association studies

Typical methods of analyzing genome-wide single nucleotide variant (SNV) data in cases and controls involve testing each variant's genotypes separately for phenotype association, and then using a substantial multiple-testing penalty to minimize the rate of false positives. This approach, however, can result in low power for modestly associated SNVs. Furthermore, simply looking at the most associated SNVs may not directly yield biological insights about disease etiology. SNVset methods attempt to address both limitations of the traditional approach by testing biologically meaningful sets of SNVs (e.g., genes or pathways). The number of tests run in a SNVset analysis is typically much lower (hundreds or thousands instead of millions) than in a traditional analysis, so the false-positive rate is lower. Additionally, by testing SNVsets that are biologically meaningful finding a significant set may more quickly yield insights into disease etiology.In this chapter we summarize the short history of SNVset testing and provide an overview of the many recently proposed methods. Furthermore, we provide detailed step-by-step instructions on how to perform a SNVset analysis, including a substantial number of practical tips and questions that researchers should consider before undertaking a SNVset analysis. Lastly, we describe a companion R package (snvset) that implements recently proposed SNVset methods. While SNVset testing is a new approach, with many new methods still being developed and many open questions, the promise of the approach is worth serious consideration when considering analytic methods for GWAS.

Haplotype kernel association test as a powerful method to identify chromosomal regions harboring uncommon causal variants

For most complex diseases, the fraction of heritability that can be explained by the variants discovered from genome-wide association studies is minor. Although the so-called "rare variants" (minor allele frequency [MAF] < 1%) have attracted increasing attention, they are unlikely to account for much of the "missing heritability" because very few people may carry these rare variants. The genetic variants that are likely to fill in the "missing heritability" include uncommon causal variants (MAF < 5%), which are generally untyped in association studies using tagging single-nucleotide polymorphisms (SNPs) or commercial SNP arrays. Developing powerful statistical methods can help to identify chromosomal regions harboring uncommon causal variants, while bypassing the genome-wide or exome-wide next-generation sequencing. In this work, we propose a haplotype kernel association test (HKAT) that is equivalent to testing the variance component of random effects for distinct haplotypes. With an appropriate weighting scheme given to haplotypes, we can further enhance the ability of HKAT to detect uncommon causal variants. With scenarios simulated according to the population genetics theory, HKAT is shown to be a powerful method for detecting chromosomal regions harboring uncommon causal variants.

Novel high-speed droplet-allele specific-polymerase chain reaction: application in the rapid genotyping of single nucleotide polymorphisms

BACKGROUND

Single nucleotide alterations such as single nucleotide polymorphisms (SNP) and single nucleotide mutations are associated with responses to drugs and predisposition to several diseases, and they contribute to the pathogenesis of malignancies. We developed a rapid genotyping assay based on the allele-specific polymerase chain reaction (AS-PCR) with our droplet-PCR machine (droplet-AS-PCR).

METHODS

Using 8 SNP loci, we evaluated the specificity and sensitivity of droplet-AS-PCR. Buccal cells were pretreated with proteinase K and subjected directly to the droplet-AS-PCR without DNA extraction. The genotypes determined using the droplet-AS-PCR were then compared with those obtained by direct sequencing.

RESULTS

Specific PCR amplifications for the 8 SNP loci were detected, and the detection limit of the droplet-AS-PCR was found to be 0.1-5.0% by dilution experiments. Droplet-AS-PCR provided specific amplification when using buccal cells, and all the genotypes determined within 9 min were consistent with those obtained by direct sequencing.

CONCLUSIONS

Our novel droplet-AS-PCR assay enabled high-speed amplification retaining specificity and sensitivity and provided ultra-rapid genotyping. Crude samples such as buccal cells were available for the droplet-AS-PCR assay, resulting in the reduction of the total analysis time. Droplet-AS-PCR may therefore be useful for genotyping or the detection of single nucleotide alterations.