DNA damage is inversely associated to blood levels of DHA and EPA fatty acids in Brazilian children and adolescents

Human Nutrition Research in the Data Era: Results of 11 Reports on the Effects of a Multiple-Micronutrient-Intervention Study

Large datasets have been used in molecular and genetic research for decades, but only a few studies have included nutrition and lifestyle factors. Our team conducted an n-of-1 intervention with 12 vitamins and five minerals in 9- to 13-year-old Brazilian children and teens with poor healthy-eating indices. A unique feature of the experimental design was the inclusion of a replication arm. Twenty-six types of data were acquired including clinical measures, whole-genome mapping, whole-exome sequencing, and proteomic and a variety of metabolomic measurements over two years. A goal of this study was to use these diverse data sets to discover previously undetected physiological effects associated with a poor diet that include a more complete micronutrient composition. We summarize the key findings of 11 reports from this study that (i) found that LDL and total cholesterol and fasting glucose decreased in the population after the intervention but with inter-individual variation; (ii) associated a polygenic risk score that predicted baseline vitamin B12 levels; (iii) identified metabotypes linking diet intake, genetic makeup, and metabolic physiology; (iv) found multiple biomarkers for nutrient and food groups; and (v) discovered metabolites and proteins that are associated with DNA damage. This summary also highlights the limitations and lessons in analyzing diverse omic data.

Identifying and Analyzing Topic Clusters in a Nutri-, Food-, and Diet-Proteomic Corpus Using Machine Reading

Nutrition affects the early stages of disease development, but the mechanisms remain poorly understood. High-throughput proteomic methods are being used to generate data and information on the effects of nutrients, foods, and diets on health and disease processes. In this report, a novel machine reading pipeline was used to identify all articles and abstracts on proteomics, diet, food, and nutrition in humans. The resulting proteomic corpus was further analyzed to produce seven clusters of "thematic" content defined as documents that have similar word content. Examples of publications from several of these clusters were then described in a similar way to a typical descriptive review.

Metabonomic analysis of follicular fluid in patients with diminished ovarian reserve

BACKGROUND

Ovarian reserve is an important factor determining female reproductive potential. The number and quality of oocytes in patients with diminished ovarian reserve (DOR) are reduced, and even if in vitro fertilization-embryo transfer (IVF-ET) is used to assist their pregnancy, the clinical pregnancy rate and live birth rate are still low. Infertility caused by reduced ovarian reserve is still one of the most difficult clinical problems in the field of reproduction. Follicular fluid is the microenvironment for oocyte survival, and the metabolic characteristics of follicular fluid can be obtained by metabolomics technology. By analyzing the metabolic status of follicular fluid, we hope to find the metabolic factors that affect the quality of oocytes and find new diagnostic markers to provide clues for early detection and intervention of patients with DOR.

METHODS

In this research, 26 infertile women with DOR and 28 volunteers with normal ovarian reserve receiving IVF/ET were recruited, and their follicular fluid samples were collected for a nontargeted metabonomic study. The orthogonal partial least squares discriminant analysis model was used to understand the separation trend of the two groups, KEGG was used to analyze the possible metabolic pathways involved in differential metabolites, and the random forest algorithm was used to establish the diagnostic model.

RESULTS

12 upregulated and 32 downregulated differential metabolites were detected by metabolic analysis, mainly including amino acids, indoles, nucleosides, organic acids, steroids, phospholipids, fatty acyls, and organic oxygen compounds. Through KEGG analysis, these metabolites were mainly involved in aminoacyl-tRNA biosynthesis, tryptophan metabolism, pantothenate and CoA biosynthesis, and purine metabolism. The AUC value of the diagnostic model based on the top 10 metabolites was 0.9936.

CONCLUSION

The follicular fluid of patients with DOR shows unique metabolic characteristics. These data can provide us with rich biochemical information and a research basis for exploring the pathogenesis of DOR and predicting ovarian reserve function.

Decreased fatty acids induced granulosa cell apoptosis in patients with diminished ovarian reserve

PURPOSE

To investigate whether fatty acid changes in granulosa cells (GCs) underly the pathogenic mechanisms of diminished ovarian reserve (DOR).

METHODS

GCs were obtained from patients with DOR (n = 70) and normal ovarian reserve (NOR, n = 70). Analysis of fatty acids changes in GCs was then analyzed.

RESULTS

Patients with DOR had significantly lower levels of antral follicle count and anti-Mullerian hormone and higher levels of follicle-stimulating hormone compared with NOR patients (P < 0.001). The good-quality embryo rate was notably decreased in DOR patients (51.99 vs 39.52%, P < 0.05). A total of 15 significantly decreased fatty acids in GCs from patients with DOR. The ATP levels were markedly lower in DOR patients than in NOR patients (39.07 ± 12.89 vs 23.21 ± 13.69%, P < 0.05). Mitochondrial membrane potential decreased in DOR patients (P < 0.01). In GCs from DOR patients, the β-oxidation genes (HADHA and ACSL) and DNA repair genes (PRKDC and RAD50) were significantly downregulated (P < 0.05). The γH2AX foci/nucleus ratio in DOR patients markedly increased relative to that of NOR patients (0.31 ± 0.03 vs 0.87 ± 0.07, P < 0.001). Meanwhile, the apoptosis rate of GCs was significantly higher in DOR patients (6.43 ± 2.11 vs 48.06 ± 6.72%, P < 0.01).

CONCLUSION

GC apoptosis resulting from the decrease of fatty acids, and associated with reduced ATP production and DNA damage, may contribute to the pathogenic mechanisms responsible for DOR.

DNA Damage, n-3 Long-Chain PUFA Levels and Proteomic Profile in Brazilian Children and Adolescents

Fatty acids play a significant role in maintaining cellular and DNA protection and we previously found an inverse relationship between blood levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and DNA damage. The aim of this study was to explore differences in proteomic profiles, for 117 pro-inflammatory proteins, in two previously defined groups of individuals with different DNA damage and EPA and DHA levels. Healthy children and adolescents (n = 140) aged 9 to 13 years old in an urban area of Brazil were divided by k-means cluster test into two clusters of DNA damage (tail intensity) using the comet assay (cluster 1 = 5.9% ± 1.2 and cluster 2 = 13.8% ± 3.1) in our previous study. The cluster with higher DNA damage and lower levels of DHA (6.2 ± 1.6 mg/dL; 5.4 ± 1.3 mg/dL, p = 0.003) and EPA (0.6 ± 0.2 mg/dL; 0.5 ± 0.1 mg/dL, p < 0.001) presented increased expression of the proteins CDK8-CCNC, PIK3CA-PIK3R1, KYNU, and PRKCB, which are involved in pro-inflammatory pathways. Our findings support the hypothesis that low levels of n-3 long-chain PUFA may have a less protective role against DNA damage through expression of pro-inflammatory proteins, such as CDK8-CCNC, PIK3CA-PIK3R1, KYNU, and PRKCB.

Contribution of genetic ancestry and polygenic risk score in meeting vitamin B12 needs in healthy Brazilian children and adolescents

Polymorphisms in genes related to the metabolism of vitamin B12 haven’t been examined in a Brazilian population. To (a) determine the correlation between the local genetic ancestry components and vitamin B12 levels using ninety B12-related genes; (b) determine associations between these genes and their SNPs with vitamin B12 levels; (c) determine a polygenic risk score (PRS) using significant variants. This cross-sectional study included 168 children and adolescents, aged 9–13 years old. Total cobalamin was measured in plasma. Genotyping arrays and whole exome data were combined to yield ~ 7000 SNPs in 90 genes related to vitamin B12. The Efficient Local Ancestry Inference was used to estimate local ancestry for African (AFR), Native American, and European (EUR). The association between the genotypes and vitamin B12 levels were determined with generalized estimating equation. Vitamin B12 levels were driven by positive (EUR) and negative (AFR, AMR) correlations with genetic ancestry. A set of 36 variants were used to create a PRS that explained 42% of vitamin level variation. Vitamin B12 levels are influenced by genetic ancestry and a PRS explained almost 50% of the variation in plasma cobalamin in Brazilian children and adolescents.