Transcriptomic analysis reveals the lipid metabolism-related gene regulatory characteristics and potential therapeutic agents for myocardial ischemia-reperfusion injury

Background

Impaired energy balance caused by lipid metabolism dysregulation is an essential mechanism of myocardial ischemia-reperfusion injury (MI/RI). This study aims to explore the lipid metabolism-related gene (LMRG) expression patterns in MI/RI and to find potential therapeutic agents.

Methods

Differential expression analysis was performed to screen the differentially expressed genes (DEGs) and LMRGs in the MI/RI-related dataset GSE61592. Enrichment and protein-protein interaction (PPI) analyses were performed to identify the key signaling pathways and genes. The expression trends of key LMRGs were validated by external datasets GSE160516 and GSE4105. The corresponding online databases predicted miRNAs, transcription factors (TFs), and potential therapeutic agents targeting key LMRGs. Finally, the identified LMRGs were confirmed in the H9C2 cell hypoxia-reoxygenation (H/R) model and the mouse MI/RI model.

Results

Enrichment analysis suggested that the "lipid metabolic process" was one of the critical pathways in MI/RI. Further differential expression analysis and PPI analysis identified 120 differentially expressed LMRGs and 15 key LMRGs. 126 miRNAs, 55 TFs, and 51 therapeutic agents were identified targeting these key LMRGs. Lastly, the expression trends of Acadm, Acadvl, and Suclg1 were confirmed by the external datasets, the H/R model and the MI/RI model.

Conclusion

Acadm, Acadvl, and Suclg1 may be the key genes involved in the MI/RI-related lipid metabolism dysregulation; and acting upon these factors may serve as a potential therapeutic strategy.

Development of a Novel Lipid Metabolism-related Gene Prognostic Signature for Patients with Colorectal Cancer

BACKGROUND

The purpose of this study was to explore the expression profiles of lipid metabolism-related genes in patients with Colorectal Cancer (CRC).

METHODS

The lipid metabolism statuses of CRC patients from The Cancer Genome Atlas (TCGA) were analyzed. Risk characteristics were constructed by univariate Cox regression and minimum Absolute contraction and Selection Operator (LASSO) Cox regression. A histogram was constructed based on factors such as age, sex, TNM stage, T stage, N stage, and risk score to provide a visual tool for clinicians to predict the probability of 1-year, 3-year, and 5-year OS for CRC patients. By determining Area Under Curve (AUC) values, the time-dependent Receiver Operating characteristic Curve (ROC) was used to evaluate the efficiency of our model in predicting prognosis.

RESULTS

A novel risk signal based on lipid metabolism-related genes was constructed to predict the survival of CRC patients. Risk characteristics were shown to be an independent prognostic factor in CRC patients (p <0.001). There were significant differences in the abundance and immune characteristics of tumor-filtering immune cells between high-risk and low-risk groups. The nomogram had a high potential for clinical application and the ROC AUC value was 0.827. Moreover, ROC analysis demonstrated that the nomogram model was more accurate to predict the survival of CRC patients than age, gender, stage and risk score.

CONCLUSION

In this study, we demonstrated a lipid metabolism-related genes prognosis biomarker associated with the tumor immune micro-environment in patients with CRC.

Evidence of association between single-nucleotide polymorphisms in lipid metabolism-related genes and type 2 diabetes mellitus in a Chinese population

Background: Type 2 diabetes mellitus (T2DM) is a complex chronic metabolic disorder triggered by insulin resistance in peripheral tissues. Evidence has shown that lipid metabolism and related genetic factors lead to insulin resistance. Hence, it is meaningful to investigate the association between single-nucleotide polymorphisms (SNPs) in lipid metabolism-related genes and T2DM. Methods: A total of 1,194 subjects with T2DM and 1,274 Non-diabetic subjects (NDM) were enrolled. Five SNPs in three genes (rs864745 in JAZF1, rs35767 in IGF1, and rs4376068, rs4402960, and rs6769511 in IGF2BP2) that contribute to insulin resistance involving lipid metabolism were genotyped using the MassArray method in a Chinese population. Results: The allele and genotypes of rs6769511 in IGF2BP2 were associated with T2DM (P=0.009 and P=0.002, respectively). In inheritance model analysis, compared with the T/T-C/T genotype, the C/C genotype of rs6769511 in IGF2BP2 was a risk factor for the development of T2DM (P<0.001, odds ratio [OR] =1.76; 95% confidence interval [CI]: 1.29-2.42). Haplotype analysis revealed associations of the rs4376068-rs4402960-rs6769511 haplotypes in IGF2BP2 with the development of T2DM (P=0.015). Additionally, rs4376068C-rs4402960T-rs6769511C was a risk haplotype for T2DM (OR=1.179; 95% CI: 1.033-1.346). Conclusion: The rs6769511 in IGF2BP2 was associated with T2DM susceptibility, and the rs4376068-rs4402960-rs6769511 haplotypes in IGF2BP2 was associated with the development of T2DM in a Chinese population.

Characterization of Growth, Fat Deposition, and Lipid Metabolism-Related Gene Expression in Lean and Obese Meat-Type Chickens

Excessive fat deposition adversely affects poultry production. In this study, we investigated growth, fat deposition, and hepatic mRNA expression of 13 lipid metabolism-related genes in three unique breeds of meat-type chickens with distinct breed origins and genetic relationships. One was Nagoya (NAG), a native Japanese breed, whereas the others were White Plymouth Rock (WPR) and White Cornish (WC), which have been used worldwide as the parental breeds of common broiler chickens. NAG chickens were phenotypically characterized by slow growth, lean body fat, and high gizzard and liver weights. In contrast, both WC and WPR chickens were characterized by rapid growth but high percentage of subcutaneous fat and abdominal fat weight, resulting from high feed intake. Among the three breeds, WC had the highest percentage of pectoral muscle weight, whereas WPR was the most obese. Among lipid metabolism-related genes, the expression of PPARA, PPARG, and CD36 was mostly associated with obesity. These results provide basic information for quantitative trait locus (QTL) analysis related to growth and fat traits in an F₂ population of the lean NAG breed and the obese WPR breed of meat-type chickens in future.

Age-Dependent Expression of MyHC Isoforms and Lipid Metabolism-Related Genes in the Longissimus Dorsi Muscle of Wild and Domestic Pigs

This study aimed to compare age-dependent changes in the relative expression of genes encoding myosin heavy chain (MyHC) isoforms and selected lipid metabolism-related genes in the longissimus dorsi muscle of wild pigs (WPs) and domestic pigs (DPs). Muscles sampled from postnatal day one as well as three-week-old and two-year-old animals were used in quantitative polymerase chain reaction (qPCR) assays, histological evaluations of succinate dehydrogenase (SDH) activity, and intra-myofiber lipid (IMFL) assessment. Expression of the MyHC isoforms displayed the most extensive age- and breed-dependent changes within the first three postnatal weeks. The MyHC_embry level decreased significantly faster in the WPs than in the DPs. The relative MyHC-I and -IIa expression was significantly higher in the WPs, and MyHC-IIb was substantially higher in the DPs. The differences in MyHC expression corroborated the number of SDH-positive myofibers and IMFLs. Expression of the peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α), peroxisome proliferator-activated receptor gamma (PPARγ) and lipoprotein lipase (LPL) genes displayed only age-related variations. In summary, the evidence is provided for accelerated postnatal myofiber transformation directed towards oxidative myofibers in WPs. The SDH activity/staining intensity largely reflected the expression of MyHCs, and not genes involved in lipid uptake and utilization.

Identification of a proliferator-activated receptor-γ antagonist for the treatment of type 2 diabetes mellitus

In the present study, a novel antagonist of the peroxisome proliferator-activated receptor-γ (PPARγ) was screened and identified, and a cell-based evaluation of the biological activity of this PPARγ antagonist was conducted. The aim of the study was to produce results that may provide a foundation for the development of a novel compound in the treatment of type 2 diabetes mellitus. Since obesity is the main cause of insulin resistance and type 2 diabetes, identifying a new reagent that is able to inhibit adipocyte differentiation and lipid accumulation is a feasible method of developing novel anti-diabetes drugs. The PPARγ antagonist was screened using a mammalian one-hybrid system and transcriptional activation. The effects of the compound on adipocyte differentiation were investigated by staining the preadipocytes with Oil Red O. In addition, the effects of the compound on the expression levels of genes associated with lipid metabolism were detected using quantitative polymerase chain reaction on differentiated mature 3T3-L1 adipocytes. As a PPARγ antagonist, N-((1H-benzo[d]imidazol-2-yl)methyl) aniline (Compound Q) was shown to depress the transcriptional activity and coactivator recruitment of PPARγ, as well as preadipocyte differentiation, in a concentration-dependent manner. The compound was also shown to decrease the expression levels of genes associated with PPARγ-regulated lipid metabolism. In conclusion, the compound screening platform was demonstrated to be valid, and the present study identified a novel PPARγ antagonist that was shown to effectively reduce the rate of adipocyte differentiation and the expression of genes associated with lipid metabolism.

No evidence of association between variant rs2075650 in lipid metabolism-related locus APOE/TOMM40 and advanced age-related macular degeneration in Han Chinese population

Age-related macular degeneration (AMD) is a late-onset, neurodegenerative disease. Genes related to lipid metabolism are important in AMD pathogenesis. Recently, a variant rs2075650 located in lipid metabolism-related locus APOE/TOMM40 was identified to be associated with advanced AMD and early AMD, respectively, in two genome-wide association studies with European ancestry, while no association study between rs2075650 and overall advanced AMD in Chinese population has been conducted before. We evaluated the potential effect of this variant on advanced AMD in a Han Chinese cohort with 204 advanced AMD patients and 1536 healthy controls. The results suggested that rs2075650 was neither associated with advanced AMD in allele level (P = 0.348) nor in genotype level (P = 0.890 under additive model with age and sex adjusted). In conclusion, our study did not confirm the impact of rs2075650 on advanced AMD risk, indicating that rs2075650 is unlikely a superior marker for APOE/TOMM40 susceptible region with advanced AMD in Han Chinese population.