Analysis of Differentially Expressed Genes in Gastrocnemius Muscle between DGAT1 Transgenic Mice and Wild-Type Mice

Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs

Simple Summary

Copy number variation (CNV) is a type of variant that may influence meat quality of, for example intramuscular fat (IMF). In this study, a genome-wide association study (GWAS) was then performed between CNVs and IMF in a pig F2 resource population. A total of 19 CNVRs were found to be significantly associated with IMF. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings.

Abstract

Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality. In this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. In conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings.

Role of diacylglycerol O-acyltransferase (DGAT) isoforms in bovine hepatic fatty acid metabolism

Fatty acid accumulation in hepatocytes induced by high concentrations of fatty acids due to lipolysis and the associated oxidative damage they cause occur most frequently after calving. Because of their role in esterification of fatty acids, diacylglycerol acyltransferase isoforms (DGAT1 and DGAT2) could play a role in the susceptibility of dairy cows to develop fatty liver. To gain mechanistic insights, we performed in vivo and in vitro analyses using liver biopsies or isolated primary hepatocytes. The in vivo study (n = 5 cows/group) involved healthy cows [average liver triacylglycerol (TAG) = 0.78%; 0.58 to 0.93%, ratio of triglyceride weight to wet liver weight] or cows diagnosed with fatty liver (average TAG = 7.60%; 5.31 to 10.54%). In vitro, hepatocytes isolated from 3 healthy female calves (1 d old, 44 to 53 kg) were challenged with (fatty acids) or without (control) a 1.2 mM mixture of fatty acids in an attempt to induce metabolic stress. Furthermore, hepatocytes were treated with DGAT1 inhibitor or DGAT2 inhibitor for 2 h followed by a challenge with (DGAT1 inhibitor + fatty acids or DGAT2 inhibitor + fatty acids) or without (DGAT1 inhibitor or DGAT2 inhibitor) the 1.2 mM mixture of fatty acids for 12 h. Data analysis of liver biopsies was compared using a 2-tailed unpaired Student's t-test. Data from calf hepatocyte treatment comparisons were assessed by one-way ANOVA, and multiplicity for each experiment was adjusted by the Holm's procedure. Data indicated that both fatty liver and in vitro challenge with fatty acids were associated with greater mRNA and protein abundance of SREBF1, FASN, DGAT1, and DGAT2. In contrast, mRNA and protein abundance of CPT1A and very low-density lipoprotein synthesis-related proteins MTTP and APOB were markedly lower. However, compared with fatty acid challenge alone, DGAT1 inhibitor + fatty acids led to greater mRNA and protein abundance of CPT1A and APOB, and greater mRNA abundance of SREBF1 and MTTP. Furthermore, this treatment led to lower mRNA abundance of FASN and DGAT2 and TAG concentrations. Compared with fatty acid challenge alone, DGAT2 inhibitor + fatty acids led to greater mRNA and protein abundance of CPT1A, MTTP, and APOB, and lower mRNA and protein abundance of SREBF1 and FASN. In addition, compared with control and fatty acids, there was greater protein abundance of GRP78 and PERK in both DGAT1 and DGAT2 inhibitor with or without fatty acids. Furthermore, compared with control and fatty acids, reactive oxygen species concentrations in the DGAT1 inhibitor with or without fatty acid group was greater. Overall, data suggested that DGAT1 is particularly relevant in the context of hepatocyte TAG synthesis from exogenous fatty acids. Disruption of both DGAT1 and DGAT2 altered lipid homeostasis, channeling fatty acids toward oxidation and generation of reactive oxygen species. Both DGAT isoforms play a role in promoting fatty acid storage into TAG and lipid droplets to protect hepatocytes from oxidative damage.

Association of DGAT1 With Cattle, Buffalo, Goat, and Sheep Milk and Meat Production Traits

Milk fatty acids are essential for many dairy product productions, while intramuscular fat (IMF) is associated with the quality of meat. The triacylglycerols (TAGs) are the major components of IMF and milk fat. Therefore, understanding the polymorphisms and genes linked to fat synthesis is important for animal production. Identifying quantitative trait loci (QTLs) and genes associated with milk and meat production traits has been the objective of various mapping studies in the last decade. Consistently, the QTLs on chromosomes 14, 15, and 9 have been found to be associated with milk and meat production traits in cattle, goat, and buffalo and sheep, respectively. Diacylglycerol O-acyltransferase 1 (DGAT1) gene has been reported on chromosomes 14, 15, and 9 in cattle, goat, and buffalo and sheep, respectively. Being a key role in fat metabolism and TAG synthesis, the DGAT1 has obtained considerable attention especially in animal milk production. In addition to milk production, DGAT1 has also been a subject of interest in animal meat production. Several polymorphisms have been documented in DGAT1 in various animal species including cattle, buffalo, goat, and sheep for their association with milk production traits. In addition, the DGAT1 has also been studied for their role in meat production traits in cattle, sheep, and goat. However, very limited studies have been conducted in cattle for association of DGAT1 with meat production traits in cattle. Moreover, not a single study reported the association of DGAT1 with meat production traits in buffalo; thus, further studies are warranted to fulfill this huge gap. Keeping in view the important role of DGAT1 in animal production, the current review article was designed to highlight the major development and new insights on DGAT1 effect on milk and meat production traits in cattle, buffalo, sheep, and goat. Moreover, we have also highlighted the possible future contributions of DGAT1 for the studied species.

The relation between serum adipose differentiation-related protein and non-alcoholic fatty liver disease in type 2 diabetes mellitus

BACKGROUND

Adipose differentiation-related protein (ADRP) is an adipokine. In vitro and animal studies have verified the role of ADRP in lipid metabolism and non-alcoholic fatty liver disease (NAFLD). The aim of this study was to evaluate the interaction between levels of ADRP and NAFLD in type 2 diabetes mellitus (T2DM).

METHODS

Cross-sectional design. A total of 142 patients with T2DM were assigned to NAFLD (Group-I) and non-NAFLD (Group-II). Anthropometric data were collected. Serum ADRP levels and biochemical parameters were also determined. t test or χ² test was conducted to compare the data between two groups. Receiver operating characteristic (ROC) curve analysis and logistic regression models were used to assess the interaction between ADRP levels and NAFLD in T2DM. Pearson correlation analysis and linear regression model were used to assess the correlations between serum ADRP levels and other parameters.

RESULTS

The serum ADRP level was higher in Group-I than in Group-II. Further, binary logistic regression models demonstrated that ADRP was an independent risk factor related to NAFLD in patients with T2DM. Moreover, as the ADRP level elevated across its tertiles, the percentage of NAFLD in T2DM increased. Multivariate logistic regression models demonstrated that the odds ratio of NAFLD was 8.831 in the highest tertile of ADRP, after adjustment for potential confounders. Area under THE ROC curve of ADRP for predicting the presence of NAFLD in T2DM was 0.738. Finally, multiple stepwise regression analysis indicated that age, waist circumference (WC), homeostasis model assessment of insulin resistance index (HOMA-IR) and triglyceride (TG) were independent factors associated with ADRP levels.

CONCLUSION

High serum ADRP level may be used as an independent risk factor for NAFLD in T2DM. The expression of ADRP may be affected by age, WC, HOMA-IR and TG.

TMT-labeled quantitative proteomic analyses on the longissimus dorsi to identify the proteins underlying intramuscular fat content in pigs

The Laiwu pig is famous for its excessively extremely high level of intramuscular fat content (IMF), however, the exact regulatory mechanism underlying intramuscular fat deposition in skeletal muscle is still unknown. As an economically important trait in pigs, IMF is controlled by multiple genes and biological pathways. In this study, we performed an integrated transcriptome-assisted TMT-labeled quantitative proteomic analysis of the longissimus dorsi (LD) muscle in Laiwu pigs at the fastest IMF deposition stage and identified 5074 unique proteins and 52 differentially abundant proteins (DAPs) (>1.5-fold cutoff, p < .05). These DAPs were hierarchically clustered in the LD muscle over two developmental stages from 120 d to 240 d. A comparison between transcriptomic (mRNA) and proteomic data revealed two differentially expressed genes corresponding to the DAPs. Changes in the levels of the nine proteins were further analyzed using RT-qPCR and parallel reaction monitoring (PRM). The proteins identified in this study could serve as candidates for elucidating the molecular mechanism of IMF deposition in pigs. SIGNIFICANCE: The intramuscular fat content (IMF) refers to the amount of fat within muscles and plays an important role in meat quality by affecting meat quality-related traits, such as tenderness, juiciness and flavor. Using the integrated transcriptome-assisted TMT-labeled quantitative proteomic approach to characterize changes in the proteomic profile of the longissimus dorsi muscle, we identified differentially abundant proteins, such as ALDH1B1, OTX2, AnxA6 and Zfp512, that are associated with intramuscular fat deposition and fat biosynthesis in pigs. These proteins could serve as candidates for elucidating the molecular mechanism of IMF deposition in pigs.

The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken

Scope: As DNA methylation is one of the key epigenetic mechanisms involved in embryonic muscle development, elucidating its relationship with non-coding RNAs and genes is essential for understanding early muscle development. The methylome profiles of pre-hatching chicken across multiple developmental stages remain incomplete although several related studies have been reported. Methods: In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq of broilers and layers in different embryonic development points (E10, E13, E16 and E19) to explore the genetic basis of embryonic muscle development in chicken. The differential methylated regions and novel lncRNAs were identified for association analyses. Through genomic position and correlation analysis between DMRs and lncRNAs, the target lncRNAs were detected to participate in the embryonic muscle formation and the results were then verified in vitro experiments. Results: Comparison of methylome profiles between two chicken lines revealed that lower methylation in broilers might contribute to muscle development in embryonic period. Differential methylated region analysis showed that the majority of differential methylated regions were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, we identified a long non-coding RNA MyH1-AS that potentially regulated embryonic muscle development, proved by the regulatory network construction and further in vitro experiments. Conclusion: Our study revealed an integrative landscape of middle- to late-stage of embryonic myogenesis in chicken, gave rise to a comprehensive understanding of epigenetic and transcriptional regulation in muscle development. Moreover, we provided a reliable data resource for further embryonic muscle development studies.

Muscle-specific Perilipin2 down-regulation affects lipid metabolism and induces myofiber hypertrophy

BACKGROUND

Perilipin2 (Plin2) belongs to a family of five highly conserved proteins, known for their role in lipid storage. Recent data indicate that Plin2 has an important function in cell metabolism and is involved in several human pathologies, including liver steatosis and Type II diabetes. An association between Plin2 and lower muscle mass and strength has been found in elderly and inactive people, but its function in skeletal muscle is still unclear. Here, we addressed the role of Plin2 in adult muscle by gain and loss of function experiments.

METHODS

By mean of in vivo Plin2 down-regulation (shPlin2) and overexpression (overPlin2) in murine tibialis anterior muscle, we analysed the effects of Plin2 genetic manipulations on myofiber size and lipid composition. An analysis of skeletal muscle lipid composition was also performed in vastus lateralis samples from young and old patients undergoing hip surgery.

RESULTS

We found that Plin2 down-regulation was sufficient to induce a 30% increase of myofiber cross-sectional area, independently of mTOR pathway. Alterations of lipid content and modulation of genes involved in lipid synthesis occurred in hypertrophic muscles. In particular, we showed a decrease of triglycerides, ceramides, and phosphatidylcoline:phosphatidylethanolamine ratio, a condition known to impact negatively on muscle function. Plin2 overexpression did not change fibre size; however, lipid composition was strongly affected in a way that is similar to that observed in human samples from old patients.

CONCLUSIONS

Altogether these data indicate that Plin2 is a critical mediator for the control of muscle mass, likely, but maybe not exclusively, through its critical role in the regulation of intracellular lipid content and composition.

ZBTB16 and metabolic syndrome: a network perspective

Metabolic syndrome is a prevalent, complex condition. The search for genetic determinants of the syndrome is currently undergoing a paradigm enhancement by adding systems genetics approaches to association studies. We summarize the current evidence on relations between an emergent new candidate, zinc finger and BTB domain containing 16 (ZBTB16) transcription factor and the major components constituting the metabolic syndrome. Information stemming from studies on experimental models with altered Zbtb16 expression clearly shows its effect on adipogenesis, cardiac hypertrophy and fibrosis, lipid levels and insulin sensitivity. Based on current evidence, we provide a network view of relations between ZBTB16 and hallmarks of metabolic syndrome in order to elucidate the potential functional links involving the ZBTB16 node. Many of the identified genes interconnecting ZBTB16 with all or most metabolic syndrome components are linked to immune function, inflammation or oxidative stress. In summary, ZBTB16 represents a promising pleiotropic candidate node for metabolic syndrome.

ZBTB16 Gene Variability Influences Obesity-Related Parameters and Serum Lipid Levels in Czech Adults

The data derived from rat models and the preliminary results of human studies provide strong indices of involvement of common ZBTB16 variants in a range of cardiovascular and metabolic traits. This cross-sectional study in the Caucasian cohort of 1517 Czech adults aimed to verify the hypothesis that ZBTB16 gene variation directly affects obesity and serum lipid levels. Genotyping of nine polymorphisms of the ZBTB16 gene (rs11214863, rs593731, rs763857, rs2846027, rs681200, rs686989, rs661223, rs675044, rs567057) was performed. A multivariate bidirectional regression with the reduction of dimensionality (O2PLS model) revealed relationships between basal lipid levels and anthropometric parameters and some minor ZBTB16 alleles. In men, the predictors – age and presence of minor ZBTB16 alleles of rs686989, rs661223, rs675044, rs567057 – were associated with significantly higher body mass index, waist to hip ratio, body adiposity index, waist and abdominal circumferences, higher total cholesterol and LDL cholesterol and explained 20 % of variability of these variables. In women, the predictors – age and presence of the rs686989 minor T allele – were also associated with increased anthropometric parameters and total cholesterol and LDL cholesterol but the obtained O2PLS model explained only 7.8 % of the variability of the explained variables. Our study confirmed that the selected gene variants of the transcription factor ZBTB16 influence the obesity-related parameters and lipid levels. This effect was more pronounced in men.