Association of polymorphisms in 5-HTT (SLC6A4) and MAOA genes with measures of obesity in young adults of Portuguese origin

Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis

Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next-generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analyses of DEGs were performed. Then, a protein-protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst databaseswereused to construct the targeted microRNAs (miRNAs), transcription factors (TFs), and small drug molecules. Finally, receiver operating characteristic (ROC) curve analysis was used to validate the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process, and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8, and EFHC2 were selected. Cyclothiazide and rotigotinethe are predicted small drug molecules for IPF treatment. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.

Genetic Correlates as a Predictor of Bariatric Surgery Outcomes after 1 Year

This study analyzed genetic risk assessments in patients undergoing bariatric surgery to serve as a predictive factor for weight loss parameters 1 year after the operation. Thirty (30) patients were assessed for Genetic Addiction Risk Severity (GARS), which analyzes neurogenetic polymorphisms involved in addiction and reward deficiency. Genetic and psychosocial data collected before the operation were correlated with weight loss data, including changes in weight, body mass index (BMI), and percent of expected weight loss (%EWL). Results examined correlations between individual gene risk alleles, 1-year body weight data, and psychosocial trait scores. Spearman's correlations revealed that the OPRM1 (rs1799971) gene polymorphism had significant negative correlation with 1-year weight (rs = -0.4477, p < 0.01) and BMI (rs = -0.4477, p < 0.05). In addition, the DRD2 risk allele (rs1800497) was correlated negatively with BMI at 1 year (rs = -0.4927, p < 0.05), indicating that one risk allele copy was associated with lower BMI. However, this allele was positively correlated with both ∆Weight (rs = 0.4077, p < 0.05) and %EWL (rs = 0.5521, p < 0.05) at 1 year post-surgery. Moreover, the overall GARS score was correlated with %EWL (rs = 0.4236, p < 0.05), ∆Weight (rs = 0.3971, p < 0.05) and ∆BMI (rs = 0.3778, p < 0.05). Lastly, Food Cravings Questionnaire (FCQ) scores were negatively correlated with %EWL (rs = -0.4320, p < 0.05) and ∆Weight at 1 year post-surgery (rs = -0.4294, p < 0.05). This suggests that individuals with a higher genetic addiction risk are more responsive to weight loss treatment, especially in the case of the DRD2 polymorphism. These results should translate clinically to improve positivity and attitude related to weight management by those individuals born with the risk alleles (rs1800497; rs1799971).

Ecology, the pace-of-life, epistatic selection and the maintenance of genetic variation in life-history genes

Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.

Association study of common functional genetic polymorphisms in SLC6A4 (5-HTT) and MAOA genes with obesity in portuguese children

OBJECTIVES

To investigate the association of polymorphisms in SLC6A4 and MAOA genes with obesity indices in children.

MATERIAL AND METHODS

A total of 637 Portuguese children (317 girls; 320 boys) aged 3-11 years-old were genotyped for the SLC6A4 polymorphisms, 5-HTTLPR and STin2, and for a MAOA VNTR. Polymorphisms were analysed by PCR-based methods.

RESULTS

Although non-significant (p = .089), our study revealed the Stin2 10 minor allele with a marked higher frequency in girls with overweight/obesity (0.466) in comparison with controls (0.376). Combining the two SLC6A4 polymorphisms, haplotype S/12 revealed in girls significant or nominally significant protective effects against BMI (β = -0.615; p = .009), BMI Z-score (β = -0.251; p = .006), WC (β = -1.4; p = .02) and WHtR (β = -0.008; p = .04).

CONCLUSIONS

We found some evidences for the role of SLC6A4 gene in measures of childhood obesity, mainly in girls.

Whole-Genome Selective Scans Detect Genes Associated With Important Phenotypic Traits in Sheep (Ovis aries)

Sheep (Ovis aries) is one of the important livestock with diverse phenotypic traits. However, little is known about the molecular mechanism of diverse phenotypic traits in domestic sheep. Using the genome-wide high-density SNP data (600K) in 253 samples from 13 populations, we conducted the tests of selective sweeps (i.e., pairwise F_ST and XP-CLR) associated with several important phenotypic traits (e.g., tail types, horn morphology, prolificacy, coat pigmentation, ear size, milk production, meat production, body size and wool fineness). We identified strong selective signatures in previously reported (e.g., T, RXFP2, BMPR1B, TYRP1, MSRB3, TF, CEBPA, GPR21 and HOXC8) and novel genes associated with the traits, such as CERS6, BTG1, RYR3, SLC6A4, NNAT and OGT for fat deposition in the tails, FOXO4 for fertility, PTCH1 and EMX2 for ear size, and RMI1 and SCD5 for body size. Further gene annotation analysis showed that these genes were identified to be the most probable genes accounting for the diverse phenotypic traits. Our results provide novel insights into the genetic mechanisms underlying the traits and also new genetic markers for genetic improvement in sheep and other livestock.

Serotonin system genes contribute to the susceptibility to obesity in Black adolescents

OBJECTIVE

The importance of the central and peripheral serotonin systems in regulating energy balance and obesity development has been highlighted in animal models. Yet, the role of both serotonin systems has not been systematically assessed in humans. The purpose of this study was to investigate the association of genes within both serotonin systems with obesity outcomes in black adolescents.

METHODS

African-American adolescents (n = 1052) whose mothers participated the Memphis New Mother's Study were assessed. In total, 110 polymorphisms mapped to 10 serotonin genes were examined for their associations with standardized body mass index (BMI-z) scores and waist circumferences using generalized estimating equation models.

RESULTS

Over 39% of adolescents were overweight or had obesity. Three single nucleotide polymorphisms (SNPs) within TPH2, HTR3B, and SLC6A4, were significantly associated with BMI-z scores (p < 1.7 × 10-3). Two SNPs in TPH2 were nominally associated with waist circumferences. One SNP in HTR2C was associated with BMI-z scores (p = 0.001) and waist circumferences (p = 0.005) only in girls. Tissue-specific expression indicates that three identified genes are predominantly expressed in the brain.

CONCLUSION

The central serotonin system may play a key role in obesity development in black adolescents. Future studies are warranted to explore additional serotonin system genes and their potential obesogenic mechanisms in humans.

Pathway-based protein-protein association network to explore mechanism of α-glucosidase inhibitors from Scutellaria baicalensis Georgi against type 2 diabetes

Natural products have been widely used in the treatment of type 2 diabetes (T2D). However, their mechanisms are often obscured due to multi-components and multi-targets. The authors constructed a pathway-based protein-protein association (PPA) network for target proteins of 13 α-glucosidase inhibitors (AGIs) identified from Scutellaria baicalensis Georgi (SBG), designed to explore the underlying mechanisms. This network contained 118 nodes and 1167 connections. An uneven degree distribution and small-world property were observed, characterised by high clustering coefficient and short average path length. The PPA network had an inherent hierarchy as C(k)∼k-0.71 . It also exhibited potential weak disassortative mixing pattern, coupled with a decreased function Knn (k) and negative value of assortativity coefficient. These properties indicated that a few nodes were crucial to the network. PGH2, GNAS, MAPK1, MAPK3, PRKCA, and MAOA were then identified as key targets with the highest degree values and centrality indices. Additionally, a core subnetwork showed that chrysin, 5,8,2'-trihydroxy-7-methoxyflavone, and wogonin were the main active constituents of these AGIs, and that the serotonergic synapse pathway was the critical pathway for SBG against T2D. The application of a pathway-based protein-protein association network provides a novel strategy to explore the mechanisms of natural products on complex diseases.

Association study of variants in genes FTO, SLC6A4, DRD2, BDNF and GHRL with binge eating disorder (BED) in Portuguese women

A population based case-control study was conducted in Portuguese women with overweight/obesity to investigate the possible association of variants in genes FTO, SLC6A4, DRD2, BDNF and GHRL with binge eating disorder (BED). The distribution of seven polymorphisms was evaluated in 31 BED patients and 62 controls. No significant associations were found between polymorphisms and BED. Of interest, a markedly lower frequency of the FTO rs9939609 obesity risk A-allele was found in BED patients (0.290) in relation to the control group (0.402). Contrasting with anorexia nervosa and bulimia nervosa, our data suggest that rs9939609 A-allele has no potential role in BED.

Deciphering the Relationship between Obesity and Various Diseases from a Network Perspective

The number of obesity cases is rapidly increasing in developed and developing countries, thereby causing significant health problems worldwide. The pathologic factors of obesity at the molecular level are not fully characterized, although the imbalance between energy intake and consumption is widely recognized as the main reason for fat accumulation. Previous studies reported that obesity can be caused by the dysfunction of genes associated with other diseases, such as myocardial infarction, hence providing new insights into dissecting the pathogenesis of obesity by investigating its associations with other diseases. In this study, we investigated the relationship between obesity and diseases from Online Mendelian Inheritance in Man (OMIM) databases on the protein–protein interaction (PPI) network. The obesity genes and genes of one OMIM disease were mapped onto the network, and the interaction scores between the two gene sets were investigated on the basis of the PPI of individual gene pairs, thereby inferring the relationship between obesity and this disease. Results suggested that diseases related to nutrition and endocrine are the top two diseases that are closely associated with obesity. This finding is consistent with our general knowledge and indicates the reliability of our obtained results. Moreover, we inferred that diseases related to psychiatric factors and bone may also be highly related to obesity because the two diseases followed the diseases related to nutrition and endocrine according to our results. Numerous obesity–disease associations were identified in the literature to confirm the relationships between obesity and the aforementioned four diseases. These new results may help understand the underlying molecular mechanisms of obesity–disease co-occurrence and provide useful insights for disease prevention and intervention.

The association of insertions/deletions (INDELs) and variable number tandem repeats (VNTRs) with obesity and its related traits and complications

BACKGROUND

Despite the fact that insertions/deletions (INDELs) are the second most common type of genetic variations and variable number tandem repeats (VNTRs) represent a large portion of the human genome, they have received far less attention than single nucleotide polymorphisms (SNPs) and larger forms of structural variation like copy number variations (CNVs), especially in genome-wide association studies (GWAS) of complex diseases like polygenic obesity. This is exemplified by the vast amount of review papers on the role of SNPs and CNVs in obesity, its related traits (like anthropometric measurements, biochemical variables, and eating behavior), and its related complications (like hypertension, hypertriglyceridemia, hypercholesterolemia, and insulin resistance-collectively known as metabolic syndrome). Hence, this paper reviews the types of INDELs and VNTRs that have been studied for association with obesity and its related traits and complications. These INDELs and VNTRs could be found in the obesity loci or genes from the earliest GWAS and candidate gene association studies, like FTO, genes in the leptin-proopiomelanocortin pathway, and UCP2/3. Given the important role of the brain serotonergic and dopaminergic reward system in obesity susceptibility, the association of INDELs and VNTRs in these neurotransmitters' metabolism and transport genes with obesity is also reviewed. Next, the role of INS VNTR in obesity and its related traits is questionable, since recent large-scale studies failed to replicate the earlier positive associations. As obesity results in chronic low-grade inflammation of the adipose tissue, the proinflammatory cytokine gene IL1RA and anti-inflammatory cytokine gene IL4 have VNTRs that are implicated in obesity. A systemic proinflammatory state in combination with activation of the renin-angiotensin system and decreased nitric oxide bioavailability as found in obesity leads to endothelial dysfunction. This explains why VNTR and INDEL in eNOS and ACE, respectively, could be predisposing factors of obesity. Finally, two novel genes, DOCK5 and PER3, which are involved in the regulation of the Akt/MAPK pathway and circadian rhythm, respectively, have VNTRs and INDEL that might be associated with obesity.

SHORT CONCLUSION

In conclusion, INDELs and VNTRs could have important functional consequences in the pathophysiology of obesity, and research on them should be continued to facilitate obesity prediction, prevention, and treatment.

The lactase -13910C>T polymorphism (rs4988235) is associated with overweight/obesity and obesity-related variables in a population sample of Portuguese young adults

BACKGROUND/OBJECTIVES

Several studies reported associations of the lactase gene (LCT) polymorphism -13910C>T (rs4988235) with obesity-related variables and obesity in adults. This study aimed to replicate previously reported associations in a population sample of Portuguese young adults.

SUBJECTS/METHODS

We genotyped 447 subjects from central and northern regions of Portugal (mean age 20.81±4.24 years) for the lactase variant -13910C>T (rs4988235), using TaqMan probes. Anthropometric variables (weight, height and body fat) were measured using standardized procedures and body mass index (BMI) (kg/m²) was calculated.

RESULTS

Frequency of genotypes was 35.8% CC (lactase nonpersistent, LNP), 48.1% CT and 16.1% TT, consistent with Hardy-Weinberg equilibrium (P=1). The frequency for the minor -13910 T allele was 0.402. Assuming a dominance model for the lactase persistence (LP) minor T-allele, linear regression models showed statistically significant associations between the LP genotype CT/TT and BMI, fat mass and weight (β=1.114, P=0.003; β=1.309, P=0.007 and β=2.67, P=0.021, respectively) after adjustment for age and sex. In concordance, logistic regression showed significant association between LP genotype CT/TT and overweight/obesity (OR=1.77; CI 1.08-2.92; P=0.023), as well as with high fat percentage ranges (OR=1.58; CI 1.01-2.46; P=0.041), when adjusting for age and sex. No significant interaction was obtained between the LCT polymorphism and physical activity for BMI (P_int=0.454) or FAT % (P_int=0.421).

CONCLUSIONS

In the Portuguese sample of young adults, the lactase -13910C>T polymorphism revealed significant associations with the obesity-related anthropometric variables BMI, fat mass and weight, and previously observed associations with the obesity risk were also confirmed.