An ACACB variant implicated in diabetic nephropathy associates with body mass index and gene expression in obese subjects

The interaction of breastfeeding and genetic factors on childhood obesity

Childhood obesity represents a pressing global public health concern due to its widespread prevalence and its close connection to early-life exposure to risk factors. The onset of obesity is contingent upon the interplay of genetic composition, lifestyle choices, and environmental as well as nutritional elements encountered during both fetal development and early childhood. This paper critically examines research discoveries in this area and concisely outlines the influence of breastfeeding on genetic predispositions associated with childhood obesity. Studies have demonstrated that breastfeeding has the potential to reduce childhood obesity by impacting anthropometric indicators. Moreover, the duration of breastfeeding is directly correlated with the degree to which it alters the risk of childhood obesity. Current explorations into the link between genetic factors transmitted through breast milk and childhood obesity predominantly focus on genes like FTO, Leptin, RXRα, PPAR-γ, and others. Numerous research endeavors have suggested that an extended period of exclusive breastfeeding is tied to a diminished likelihood of childhood obesity, particularly if sustained during the initial six months. The duration of breastfeeding also correlates with gene methylation, which could serve as the epigenetic mechanism underpinning breastfeeding's preventative influence against obesity. In summary, the thorough evaluation presented in this review underscores the intricate nature of the association between breastfeeding, genetic factors, and childhood obesity, providing valuable insights for future research efforts and policy formulation.

The effects of breastfeeding and formula feeding on the metabolic factors and the expression level of obesity and diabetes-predisposing genes in healthy infants

Diabetes mellitus (DM) and obesity are common illnesses characterized by glucose metabolism issues and excessive weight gain. Breastfeeding is the best way to feed a newborn up to 6 months old and it has been shown to reduce the risk of diabetes and obesity later in life due to its nutritional properties. The purpose of this study was to investigate the effects of breastfeeding, formula feeding, and formula-plus breastfeeding (mix-feeding) on the anthropometric indices, metabolic variables, and the expression level of obesity and diabetes-predisposing genes of healthy infants. A total of 150 healthy infants were enrolled in this cross-sectional study. All infants (aged 24 months) were divided into three groups based on the type of feeding, breastfeeding, formula feeding, and mix-feeding. The anthropometric indices, glycemic indexes, lipid profile, and the expression levels of acetyl-coenzyme A carboxylase beta (ACACB), brain-derived neurotrophic factor (BDNF), liver X receptor α (LXR-α), peroxisome proliferator-activated receptor γ (PPAR-γ), and phosphatase and tensin homolog (PTEN) genes were measured in all infants using reverse transcription-polymerase chain reaction (RT-PCR) method. The anthropometric indices including weight, height, head circumference, insulin, total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) were lower in the breastfeeding infants in comparison to other groups. As well, the expression level of the ACACB gene was significantly downregulated in breastfeeding infants, while the PPAR-γ gene was significantly upregulated, but the expression levels of LXR- α, PTEN and BDNF did not change significantly across groups. Breastfeeding compared to formula feeding had positive effects on anthropometric indices, metabolic variables, and diabetes-predisposing genes.

Acetyl-coenzyme A carboxylase beta gene polymorphism does not predict cardiovascular risk susceptibility in Chinese type 2 diabetic individuals

AIM

Type 2 diabetes (T2D) is associated with significant cardiovascular (CV) morbidity and mortality. A single-nucleotide polymorphism (SNP) in the acetyl-coenzyme A carboxylase beta (ACACB) gene, rs2268388, reproducibly associates with diabetic nephropathy (DN). ACACB regulates fatty-acid oxidation. As such, we assessed whether ACACB SNP rs2268388 was associated with CV disease in Chinese individuals with T2D.

METHODS

Chinese individuals with T2D were genotyped for SNP rs2268388. Baseline demographics were recorded and clinical data regarding coronary, carotid, and peripheral arterial disease and congestive heart failure were retrieved from electronic patient records. Statistical analyses were performed to detect associations between the rs2268388 T risk allele with CV outcomes in the cohort.

RESULTS

A total of 596 Chinese individuals with T2D were genotyped. Their mean age was 66.8 ± 10.9 years at the time of data extraction. Genotyping revealed 59.7%, 33.2% and 7.1% of the study population were non-carriers, heterozygous and homozygous carriers of the rs2268388 T risk allele in ACACB. No statistically significant correlations of the risk allele were observed with CV outcomes.

CONCLUSION

These results did not demonstrate association between rs2268388 SNP in ACACB with CV outcomes in Chinese T2D patients. The ACACB gene and its role in CV risk susceptibility, via alterations in fatty acid oxidation, remains an interesting postulate and studies with larger cohort sizes and in different ethnic groups remain warranted.

Identification of core gene in obese type 2 diabetes patients using bioinformatics analysis

Objectives Adipocytes and adipocyte lipid metabolism are closely related with obesity and type 2 diabetes, but the molecular mechanism still needs further investigation. The aim of this study is to discover the adipocyte genes and pathways involved in obesity and type 2 diabetes using bioinformatics analysis.

Methods The GSE27951 gene expression profile was obtained. Software and online tools (STRING, Cytoscape, BioGPS, CTD, and FunRich) were used to identify core genes.21 human subcutaneous adipose samples, with 10 from type 2 diabetic patients and 11 from normal controls, were included in these analyses.

Results 184 differentially expressed genes (DEGs) including 42 up-regulated genes and 142 down-regulated genes were found to be enriched in metabolism, receptor activity, collagen type IV and glutamine biosynthesis I pathway by using the enrichment analysis. Seven hub genes were identified from the PPI network using various software (Cytoscape, STRING, BioGPS, and CTD). Four core genes (COL4A2, ACACB, GLUL, and CD36) were found to be highly expressed in subcutaneous adipose tissue of obese patients accompanying type 2 diabetes.

Conclusion COL4A2, ACACB, GLUL and CD36 might be the core molecular biomarkers of obesity in patients with or without type 2 diabetes.

APOL1 Kidney-Risk Variants Induce Mitochondrial Fission

Introduction

APOL1 G1 and G2 nephropathy-risk variants cause mitochondrial dysfunction and contribute to kidney disease. Analyses were performed to determine the genetic regulation of APOL1 and elucidate potential mechanisms in APOL1-nephropathy.

Methods

A global gene expression analysis was performed in human primary renal tubule cell lines derived from 50 African American individuals. Follow-up gene knock out, cell-based rescue, and microscopy experiments were performed.

Results

APOL1 genotypes did not alter APOL1 expression levels in the global gene expression analysis. Expression quantitative trait locus (eQTL) analysis in polyinosinic-polycytidylic acid (poly IC)–stimulated renal tubule cells revealed that single nucleotide polymorphism (SNP) rs513349 adjacent to BAK1 was a trans eQTL for APOL1 and a cis eQTL for BAK1; APOL1 and BAK1 were co-expressed in cells. BAK1 knockout in a human podocyte cell line resulted in diminished APOL1 protein, supporting a pivotal effect for BAK1 on APOL1 expression. Because BAK1 is involved in mitochondrial dynamics, mitochondrial morphology was examined in primary renal tubule cells and HEK293 Tet-on cells of various APOL1 genotypes. Mitochondria in APOL1 wild-type (G0G0) tubule cells maintained elongated morphology when stimulated by low-dose poly IC, whereas those with G1G1, G2G2, and G1G2 genotypes appeared to fragment. HEK293 Tet-on cells overexpressing APOL1 G0, G1, and G2 were created; G0 cells appeared to promote mitochondrial fusion, whereas G1 and G2 induced mitochondrial fission. The mitochondrial dynamic regulator Mdivi-1 significantly preserved cell viability and mitochondrial cristae structure and reversed mitochondrial fission induced by overexpression of G1 and G2.

Conclusion

Results suggest the mitochondrial fusion/fission pathway may be a therapeutic target in APOL1-nephropathy.

Microarray Analysis of Differential Gene Expression in Alzheimer's Disease Identifies Potential Biomarkers with Diagnostic Value

BACKGROUND Alzheimer disease (AD) is a common and fatal subtype of dementia that remains a challenge to diagnose and treat. This study aimed to identify potential biomarkers that influence the prognosis of AD. MATERIAL AND METHODS A total of 6 gene expression profiles from the Gene Expression Omnibus (GEO) database were assessed for their potential as AD biomarkers. We identified differentially expressed genes (DEGs) using the prediction analysis for microarray (PAM) algorithm and obtained hub genes through the analysis of the protein-protein interaction (PPI) network and module analysis. RESULTS We identified 6 gene expression profiles from the GEO database and assessed their potential as AD biomarkers. Shared gene sets were extracted and integrated into large expression profile matrices. We identified 2514 DEGs including 68 upregulated- and 2446 downregulated genes through analysis of the limma package. We screened 379 significant DEGs including 68 upregulated and 307 downregulated genes for their ability to distinguish AD from control samples using PAM algorithm. Functional enrichment of the 379 target genes was produced from Database for Annotation, Visualization and Integrated Discovery.(DAVID) and included histone function, beta receptor signaling, cell growth, and angiogenesis. The downregulated genes were significantly enriched in MAPK signaling, synaptic signaling, neuronal apoptosis and AD associated pathways. Upon analysis of the PPI network, 32 hub genes including ENO2, CCT2, CALM2, ACACB, ATP5B, MDH1, and PP2CA were screened. Of these hub genes, NFKBIA and ACACB were upregulated and 29 genes were downregulated in AD patients. CONCLUSIONS We screened 379 significant DEGs as potential biomarkers of AD using PAM and obtained 32 hub genes through PPI network and module analysis. These findings reveal new potential AD biomarkers with prognostic and therapeutic value.

Analysis of porcine body size variation using re-sequencing data of miniature and large pigs

Background

Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in “SweepFinder”, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely F_ST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F₂ individuals from a cross of Goettingen Minipigs and large pigs.

Results

Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F₂ cross-breds.

Conclusion

The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5009-y) contains supplementary material, which is available to authorized users.

Novel polymorphisms associated with hyperalphalipoproteinemia and apparent cardioprotection

BACKGROUND

Hyperalphalipoproteinemia (HALP) is inversely correlated with coronary heart disease (CHD) although genetic variants associated with high serum levels of high-density lipoprotein cholesterol (HDL-C) have not been shown to be cardioprotective.

OBJECTIVE

The objective of the study was to uncover novel genetic variants associated with HALP and possibly with reduced risk of CHD.

METHODS

Exome sequencing data, HDL-C, and triglyceride levels were analyzed in 1645 subjects. They included the University of Maryland outpatients with high HDL-C (n = 12), Cardiovascular Health Study (n = 210), Jackson Heart Study (n = 402), Multi-Ethnic Study of Atherosclerosis (n = 404), Framingham Heart Study (n = 463), and Old Order Amish (n = 154).

RESULTS

Novel nonsynonymous single-nucleotide polymorphisms (nsSNPs) were identified in men and women with primary HALP (mean HDL-C, 145 ± 30 mg/dL). Using PolyPhen-2 and Combined Annotation Dependent Depletion to estimate the predictive effect of each nsSNP on the gene product, rare, deleterious polymorphisms in UGT1A3, PLLP, PLEKHH1, ANK2, DIS3L, ACACB, and LRP4 were identified in 16 subjects with HALP but not in any tested subject with low HDL-C (<40 mg/dL). In addition, a single novel polymorphism, rs376849274, was found in OSBPL1A. The majority of these candidate genes have been implicated in fat and lipid metabolism, and none of these subjects has a history of CHD despite 75% of subjects having risk factors for CHD. Overall, the probability of finding these nsSNPs in a non-high HDL-C population ranges from 1 × 10-17 to 1 × 10-25.

CONCLUSION

Novel functional polymorphisms in 8 candidate genes are associated with HALP in the absence of CHD. Future study is required to examine the extent to which these genes may affect HDL function and serve as potential therapeutic targets for CHD risk reduction.

In vivo Modeling Implicates APOL1 in Nephropathy: Evidence for Dominant Negative Effects and Epistasis under Anemic Stress

African Americans have a disproportionate risk for developing nephropathy. This disparity has been attributed to coding variants (G1 and G2) in apolipoprotein L1 (APOL1); however, there is little functional evidence supporting the role of this protein in renal function. Here, we combined genetics and in vivo modeling to examine the role of apol1 in glomerular development and pronephric filtration and to test the pathogenic potential of APOL1 G1 and G2. Translational suppression or CRISPR/Cas9 genome editing of apol1 in zebrafish embryos results in podocyte loss and glomerular filtration defects. Complementation of apol1 morphants with wild-type human APOL1 mRNA rescues these defects. However, the APOL1 G1 risk allele does not ameliorate defects caused by apol1 suppression and the pathogenicity is conferred by the cis effect of both individual variants of the G1 risk haplotype (I384M/S342G). In vivo complementation studies of the G2 risk allele also indicate that the variant is deleterious to protein function. Moreover, APOL1 G2, but not G1, expression alone promotes developmental kidney defects, suggesting a possible dominant-negative effect of the altered protein. In sickle cell disease (SCD) patients, we reported previously a genetic interaction between APOL1 and MYH9. Testing this interaction in vivo by co-suppressing both transcripts yielded no additive effects. However, upon genetic or chemical induction of anemia, we observed a significantly exacerbated nephropathy phenotype. Furthermore, concordant with the genetic interaction observed in SCD patients, APOL1 G2 reduces myh9 expression in vivo, suggesting a possible interaction between the altered APOL1 and myh9. Our data indicate a critical role for APOL1 in renal function that is compromised by nephropathy-risk encoding variants. Moreover, our interaction studies indicate that the MYH9 locus is also relevant to the phenotype in a stressed microenvironment and suggest that consideration of the context-dependent functions of both proteins will be required to develop therapeutic paradigms.

African Americans have a disproportionate risk for developing chronic kidney disease compared to European Americans. Previous studies have identified a region on chromosome 22 containing two genes, MYH9 and APOL1, which likely accounts for nearly all of this difference. Previous reports provided strong statistical evidence implicating APOL1 as the major contributor to nephropathy risk in African Americans, driven by two coding variants, termed G1 and G2. However, other groups still report statistical evidence for MYH9 association in kidney disease, and animal models have demonstrated biological relevance for MYH9 function in the kidney. Here, we show that suppressing apol1 in zebrafish embryos results in perturbed kidney function. Importantly, using this in vivo assay, we show that the G1 variant appears to cause a loss of APOL1 function, while the G2 variant results in an altered protein that may be acting antagonistically in the presence of normal APOL1. We also report a genetic interaction between apol1 and myh9 under anemic stress, which is consistent with our previous findings in sickle cell disease (SCD) nephropathy patients. Finally, we provide functional evidence in vivo that the G2-altered APOL1 may be interacting with MYH9 to confer nephropathy risk.

Localization of APOL1 protein and mRNA in the human kidney: nondiseased tissue, primary cells, and immortalized cell lines

Although APOL1 gene variants are associated with nephropathy in African Americans, little is known about APOL1 protein synthesis, uptake, and localization in kidney cells. To address these questions, we examined APOL1 protein and mRNA localization in human kidney and human kidney-derived cell lines. Indirect immunofluorescence microscopy performed on nondiseased nephrectomy cryosections from persons with normal kidney function revealed that APOL1 protein was markedly enriched in podocytes (colocalized with synaptopodin and Wilms' tumor suppressor) and present in lower abundance in renal tubule cells. Fluorescence in situ hybridization detected APOL1 mRNA in glomeruli (podocytes and endothelial cells) and tubules, consistent with endogenous synthesis in these cell types. When these analyses were extended to renal-derived cell lines, quantitative RT-PCR did not detect APOL1 mRNA in human mesangial cells; however, abundant levels of APOL1 mRNA were observed in proximal tubule cells and glomerular endothelial cells, with lower expression in podocytes. Western blot analysis revealed corresponding levels of APOL1 protein in these cell lines. To explain the apparent discrepancy between the marked abundance of APOL1 protein in kidney podocytes observed in cryosections versus the lesser abundance in podocyte cell lines, we explored APOL1 cellular uptake. APOL1 protein was taken up readily by human podocytes in vitro but was not taken up efficiently by mesangial cells, glomerular endothelial cells, or proximal tubule cells. We hypothesize that the higher levels of APOL1 protein in human cryosectioned podocytes may reflect both endogenous protein synthesis and APOL1 uptake from the circulation or glomerular filtrate.