Evidence of Polygenic Adaptation in the Systems Genetics of Anthropometric Traits

The Influence of the Differentiation of Genes Encoding Peroxisome Proliferator-Activated Receptors and Their Coactivators on Nutrient and Energy Metabolism

Genetic components may play an important role in the regulation of nutrient and energy metabolism. In the presence of specific genetic variants, metabolic dysregulation may occur, especially in relation to the processes of digestion, assimilation, and the physiological utilization of nutrients supplied to the body, as well as the regulation of various metabolic pathways and the balance of metabolic changes, which may consequently affect the effectiveness of applied reduction diets and weight loss after training. There are many well-documented studies showing that the presence of certain polymorphic variants in some genes can be associated with specific changes in nutrient and energy metabolism, and consequently, with more or less desirable effects of applied caloric reduction and/or exercise intervention. This systematic review focused on the role of genes encoding peroxisome proliferator-activated receptors (PPARs) and their coactivators in nutrient and energy metabolism. The literature review prepared showed that there is a link between the presence of specific alleles described at different polymorphic points in PPAR genes and various human body characteristics that are crucial for the efficacy of nutritional and/or exercise interventions. Genetic analysis can be a valuable element that complements the work of a dietitian or trainer, allowing for the planning of a personalized diet or training that makes the best use of the innate metabolic characteristics of the person who is the subject of their interventions.

Disentangling sex differences in the shared genetic architecture of posttraumatic stress disorder, traumatic experiences, and social support with body size and composition

There is a well-known association of traumatic experiences and posttraumatic stress disorder (PTSD) with body size and composition, including consistent differences between sexes. However, the biology underlying these associations is unclear. To understand the genetic underpinnings of this complex relationship, we investigated genome-wide datasets informative of African and European ancestries from the Psychiatric Genomic Consortium, the UK Biobank, the GIANT Consortium, and the Million Veteran Program. We used genome-wide association statistics to estimate sex-specific genetic correlations (r g ) of traumatic experiences, social support, and PTSD with multiple anthropometric traits. After multiple testing corrections (false discovery rate, FDR q < 0.05), we observed 58 significant r g relationships in females (e.g., childhood physical abuse and body mass index, BMI r g  = 0.245, p = 3.88 × 10-10) and 21 significant r g relationships in males (e.g., been involved in combat or exposed to warzone and leg fat percentage; r g  = 0.405, p = 4.42 × 10-10). We performed causal inference analyses of these genetic overlaps using Mendelian randomization and latent causal variable approaches. Multiple female-specific putative causal relationships were observed linking body composition/size with PTSD (e.g., leg fat percentage→PTSD; beta = 0.319, p = 3.13 × 10-9), traumatic experiences (e.g., childhood physical abuse→waist circumference; beta = 0.055, p = 5.07 × 10-4), and childhood neglect (e.g., "someone to take you to doctor when needed as a child"→BMI; beta = -0.594, p = 1.09 × 10-5). In males, we observed putative causal effects linking anthropometric-trait genetic liabilities to traumatic experiences (e.g., BMI→childhood physical abuse; beta = 0.028, p = 8.19 × 10-3). Some of these findings were replicated in individuals of African descent although the limited sample size available did not permit us to conduct a sex-stratified analysis in this ancestry group. In conclusion, our findings provide insights regarding sex-specific causal networks linking anthropometric traits to PTSD, traumatic experiences, and social support.

The polymorphisms of the PPARD gene modify post-training body mass and biochemical parameter changes in women

In this study we examined the genotype distribution of the PPARD rs2267668, rs2016520, and rs1053049 alleles in a group of women, before and after the completion of a 12-week training program. There were two significant genotype × training interactions resulting in decreases of total cholesterol (Chol) through training in rs2267668 G allele carriers and significant increases of triglyceride (TGL) levels in rs2267668 AA homozygotes. Carriers of rs2016520 PPARD C allele exhibited a significant decrease in Chol through training with an accompanying decrease in TGL. There was also overrepresentation of PPARD rs1053049 TT homozygotes in the group with higher post-training TGL levels. Moreover (rs2267668/rs2016520/rs1053049) G/C/T haplotype displayed smaller post-training body mass decrease, suggesting that harboring this specific G/C/T haplotype is unfavorable for achieving the desired training-induced body mass changes. On the other hand, the G/C/C haplotype was significantly associated with post-training increase in fat free mass (FFM) and with lower levels of Chol as well as TGL as observed in the blood of the participants in response to applied training. This observation constitutes the second important finding of the study, implying that when specific training-induced biochemical changes are taken into account, some individuals may benefit from carrying the G/C/C haplotype.

Local adaptation in European populations affected the genetics of psychiatric disorders and behavioral traits

Background

Recent studies have used genome-wide data to investigate evolutionary mechanisms related to behavioral phenotypes, identifying widespread signals of positive selection. Here, we conducted a genome-wide investigation to study whether the molecular mechanisms involved in these traits were affected by local adaptation.

Methods

We performed a polygenic risk score analysis in a sample of 2455 individuals from 23 European populations with respect to variables related to geo-climate diversity, pathogen diversity, and language phonological complexity. The analysis was adjusted for the genetic diversity of European populations to ensure that the differences detected would reflect differences in environmental exposures.

Results

The top finding was related to the association between winter minimum temperature and schizophrenia. Additional significant geo-climate results were also observed with respect to bipolar disorder (sunny daylight), depressive symptoms (precipitation rate), major depressive disorder (precipitation rate), and subjective well-being (relative humidity). Beyond geo-climate variables, we also observed findings related to pathogen diversity and language phonological complexity: openness to experience was associated with protozoan diversity; conscientiousness and extraversion were associated with language consonants.

Conclusions

We report that common variation associated with psychiatric disorders and behavioral traits was affected by processes related to local adaptation in European populations.

Electronic supplementary material

The online version of this article (10.1186/s13073-018-0532-7) contains supplementary material, which is available to authorized users.

ADH1B: From alcoholism, natural selection, and cancer to the human phenome

The ADH1B (Alcohol Dehydrogenase 1B (class I), Beta Polypeptide) gene and its best-known functional alleles, Arg48His (rs1229984, ADH1B*2) and Arg370Cys (rs2066702, ADH1B*3), have been investigated in relation to many phenotypic traits; most frequently including alcohol metabolism and alcohol drinking behaviors, but also human evolution, liver function, cancer, and, recently, the comprehensive human phenome. To understand ADH1B functions and consequences, we provide here a bioinformatic analysis of its gene regulation and molecular functions, literature review of studies focused on this gene, and a discussion regarding future research perspectives. Certain ADH1B alleles have large effects on alcohol metabolism, and this relationship particularly encourages further investigations in relation to alcoholism and alcohol-associated cancer to understand better the mechanisms by which alcohol metabolism contributes to alcohol abuse and carcinogenesis. We also observed that ADH1B has complex mechanisms that regulate its expression across multiple human tissues, and these may be involved in cardiac and metabolic traits. Evolutionary data strongly suggest that the selection signatures at the ADH1B locus are primarily related to effects other than those on alcohol metabolism. This is also supported by the involvement of ADH1B in multiple molecular pathways and by the findings of our recent phenome-wide association study. Accordingly, future studies should also investigate other functions of ADH1B potentially relevant for the human phenome. © 2017 Wiley Periodicals, Inc.

A putative causal relationship between genetically determined female body shape and posttraumatic stress disorder

Background

The nature and underlying mechanisms of the observed increased vulnerability to posttraumatic stress disorder (PTSD) in women are unclear.

Methods

We investigated the genetic overlap of PTSD with anthropometric traits and reproductive behaviors and functions in women. The analysis was conducted using female-specific summary statistics from large genome-wide association studies (GWAS) and a cohort of 3577 European American women (966 PTSD cases and 2611 trauma-exposed controls). We applied a high-resolution polygenic score approach and Mendelian randomization analysis to investigate genetic correlations and causal relationships.

Results

We observed an inverse association of PTSD with genetically determined anthropometric traits related to body shape, independent of body mass index (BMI). The top association was related to BMI-adjusted waist circumference (WC_adj; R = –0.079, P < 0.001, Q = 0.011). We estimated a relative decrease of 64.6% (95% confidence interval = 27.5–82.7) in the risk of PTSD per 1-SD increase in WC_adj. MR-Egger regression intercept analysis showed no evidence of pleiotropic effects in this association (P_pleiotropy = 0.979). We also observed associations of genetically determined WC_adj with age at first sexual intercourse and number of sexual partners (P = 0.013 and P < 0.001, respectively).

Conclusions

There is a putative causal relationship between genetically determined female body shape and PTSD, which could be mediated by evolutionary mechanisms involved in human sexual behaviors.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-017-0491-4) contains supplementary material, which is available to authorized users.

Body height and immune efficacy: testing body stature as a signal of biological quality

According to the good genes hypothesis and energy allocation theory, human adult body height may reflect biological quality. An important aspect of this quality is immune system functioning (ISF). The aim of this study was to evaluate the relationship between ISF and body height in healthy people. The ISF was determined by several important innate (total complement and lysozyme activity, neutrophil function) and adaptive immune parameters (lymphocytes, IgA and IgG, and response to the flu vaccine). Overall, 96 males and 97 females were subjected to flu vaccination, and of these, 35 males and 34 females were subjected to tetanus. Blood samples were collected before and four weeks after vaccination. Immunomodulatory factors, participant's age, body fat, and free testosterone levels, were controlled. There was no association between body height and all analysed immune parameters for both sexes. That might suggest that in Western society, a women's preference for taller men is not related to 'good genes for immune competence'. We propose the novel Immunity Priority Hypothesis that explains the lack of relationship between adult body stature and ISF. This hypothesis, however, does not contradict the signalling role of a man's body height as a morphological marker of biological quality.

Widespread signatures of positive selection in common risk alleles associated to autism spectrum disorder

The human brain is the outcome of innumerable evolutionary processes; the systems genetics of psychiatric disorders could bear their signatures. On this basis, we analyzed five psychiatric disorders, attention deficit hyperactivity disorder, autism spectrum disorder (ASD), bipolar disorder, major depressive disorder, and schizophrenia (SCZ), using GWAS summary statistics from the Psychiatric Genomics Consortium. Machine learning-derived scores were used to investigate two natural-selection scenarios: complete selection (loci where a selected allele reached fixation) and incomplete selection (loci where a selected allele has not yet reached fixation). ASD GWAS results positively correlated with incomplete-selection (p = 3.53*10⁻⁴). Variants with ASD GWAS p<0.1 were shown to have a 19%-increased probability to be in the top-5% for incomplete-selection score (OR = 1.19, 95%CI = 1.11–1.8, p = 9.56*10⁻⁷). Investigating the effect directions of minor alleles, we observed an enrichment for positive associations in SNPs with ASD GWAS p<0.1 and top-5% incomplete-selection score (permutation p<10⁻⁴). Considering the set of these ASD-positive-associated variants, we observed gene-expression enrichments for brain and pituitary tissues (p = 2.3*10⁻⁵ and p = 3*10⁻⁵, respectively) and 53 gene ontology (GO) enrichments, such as nervous system development (GO:0007399, p = 7.57*10⁻¹²), synapse organization (GO:0050808, p = 8.29*10⁻⁷), and axon guidance (GO:0007411, p = 1.81*10⁻⁷). Previous genetic studies demonstrated that ASD positively correlates with childhood intelligence, college completion, and years of schooling. Accordingly, we hypothesize that certain ASD risk alleles were under positive selection during human evolution due to their involvement in neurogenesis and cognitive ability.

Predisposition to psychiatric disorders is due to the contribution of many genes involved in numerous molecular mechanisms. Since brain evolution has played a pivotal role in determining the success of the human species, the molecular pathways involved with the onset of mental illnesses are likely to be informative as we seek an understanding of the mechanisms involved in the evolution of human brain. Accordingly, we tested whether the genetics of psychiatric disorders is enriched for signatures of positive selection. We observed a strong finding related to the genetics of autism spectrum disorders (ASD): common risk alleles are enriched for genomic signatures of incomplete selection (loci where a selected allele has not yet reached fixation). The genes where these alleles map tend to be expressed in brain and pituitary tissues, to be involved in molecular mechanisms related to nervous system development, and surprisingly, to be associated with increased cognitive ability. Previous studies identified signatures of purifying selection in genes affected by ASD rare alleles. Accordingly, at least two different evolutionary mechanisms appear to be present in relation to ASD genetics: 1) rare disruptive alleles eliminated by purifying selection; 2) common alleles selected for their beneficial effects on cognitive skills. This scenario would explain ASD prevalence, which is higher than that expected for a trait under purifying selection, as the evolutionary cost of polygenic adaptation related to cognitive ability.