iTRAQ-based quantitative proteomic analysis reveals the distinct early embryo myofiber type characteristics involved in landrace and miniature pig

Transcriptome Profiling of Different Developmental Stages on Longissimus Dorsi to Identify Genes Underlying Intramuscular Fat Content in Wannanhua Pigs

Intramuscular fat (IMF) is a key index to measure the tenderness and flavor of pork. Wannanhua pig, a famous indigenous pig breed in Anhui Province, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model for investigating the lipid position trait mechanisms in pigs. However, the regulatory mechanisms of lipid deposition and development in pigs remain unclear. Furthermore, the temporal differences in gene regulation are based on muscle growth and IMF deposition. The purpose of this study was to study the expression changes of longissimus dorsi (LD) at different growth stages of WH pigs at the molecular level, to screen the candidate genes and signaling pathways related to IMF during development by transcriptome sequencing technology, and to explore the transcriptional regulation mechanism of IMF deposition-related genes at different development stages. In total, 616, 485, and 1487 genes were differentially expressed between LD60 and LD120, LD120 and LD240, and LD60 and LD240, respectively. Numerous differentially expressed genes (DEGs) associated with lipid metabolism and muscle development were identified, and most of them were involved in IMF deposition and were significantly up-regulated in LD120 and LD240 compared to LD60. STEM (Short Time-series Expression Miner) analysis indicated significant variations in the mRNA expression across distinct muscle development stages. The differential expression of 12 selected DEGs was confirmed by RT-qPCR. The results of this study contribute to our understanding of the molecular mechanism of IMF deposition and provide a new way to accelerate the genetic improvement of pork quality.

Fetal muscle extract improves muscle function and performance in aged mice

Background: Loss of skeletal muscle mass and function is one of the major musculoskeletal health problems in the aging population. Recent studies have demonstrated differential proteomic profiles at different fetal stages, which might be associated with muscle growth and development. We hypothesized that extract derived from fetal muscle tissues at the stage of hypertrophy could ameliorate the loss of muscle mass and strength in aged mice.

Methods: To allow sufficient raw materials for investigation, skeletal muscle extract from fetal sheep at week 16 of gestation and maternal tissue were used in the present study. iTRAQ (isobaric tags for relative and absolute quantitation) and KEGG pathway analyses identified differentially expressed proteins in fetal sheep muscle extract vs. adult sheep muscle extract. Effects of FSME and ASME on human myoblast proliferation were studied. To examine the effect of FSME in vivo, C57BL/6 male mice at 20 months of age were subjected to intramuscular administration of FSME or vehicle control for 8 weeks. A grip strength test and ex vivo muscle force frequency test were conducted. Finally, serum samples were collected for multiplex analysis to determine potential changes in immunological cytokines upon FSME injection.

Results: Compared with ASME, 697 and 412 peptides were upregulated and downregulated, respectively, in FSME, as indicated by iTRAQ analysis. These peptides were highly related to muscle development, function, and differentiation from GO enrichment analysis. FSME promoted cell proliferation of myoblast cells (+300%, p < 0.01) without causing significant cytotoxicity at the tested concentration range compared with ASME. After 8 weeks of FSME treatment, the percentage of lean mass (+10%, p < 0.05), grip strength (+50%, p < 0.01), and ability in fatigue resistance were significantly higher than those of the control group. Isometric forces stimulated by different frequencies were higher in the control group. Histologically, the control group showed a larger cross-sectional area (+20%, p < 0.01) than the FSME group. The multiplex assay indicated that FSME treatment did not lead to an elevated circulatory level of inflammatory cytokines. Of note, after FSME treatment, we observed a significant drop in the circulating level of IL-12 (p40) from 90.8 ± 48.3 pg/ml to 82.65 ± 4.4 pg/ml, G-CSF from 23476 ± 8341.9 pg/ml to 28.35 ± 24.2 pg/ml, KC from 97.09 ± 21.2 pg/ml to 29.2 ± 7.2 pg/ml, and RANTES from 325.4 ± 17.3 pg/ml to 49.96 ± 32.1 pg/ml.

Conclusion: This is the first study demonstrating the beneficial effect of fetal muscle extract on muscle health in aged mice. Further analysis of the active ingredients of the extract will shed light on the development of a novel treatment for sarcopenia.

A Combined Differential Proteome and Transcriptome Profiling of Fast- and Slow-Twitch Skeletal Muscle in Pigs

Skeletal muscle fiber types can contribute in part to affecting pork quality parameters. Biceps femoris (Bf) (fast muscle or white muscle) and Soleus (Sol) (slow muscle or red muscle) are two typical skeletal muscles characterized by obvious muscle fiber type differences in pigs. However, the critical proteins and potential regulatory mechanisms regulating porcine skeletal muscle fibers have yet to be clearly defined. In this study, the isobaric Tag for Relative and Absolute Quantification (iTRAQ)-based proteome was used to identify the key proteins affecting the skeletal muscle fiber types with Bf and Sol, by integrating the previous transcriptome data, while function enrichment analysis and a protein–protein interaction (PPI) network were utilized to explore the potential regulatory mechanisms of skeletal muscle fibers. A total of 126 differentially abundant proteins (DAPs) between the Bf and Sol were identified, and 12 genes were found to be overlapping between differentially expressed genes (DEGs) and DAPs, which are the critical proteins regulating the formation of skeletal muscle fibers. Functional enrichment and PPI analysis showed that the DAPs were mainly involved in the skeletal-muscle-associated structural proteins, mitochondria and energy metabolism, tricarboxylic acid cycle, fatty acid metabolism, and kinase activity, suggesting that PPI networks including DAPs are the main regulatory network affecting muscle fiber formation. Overall, these data provide valuable information for understanding the molecular mechanism underlying the formation and conversion of muscle fiber types, and provide potential markers for the evaluation of meat quality.

The orphan GPR50 receptor interacting with TβRI induces G1/S-phase cell cycle arrest via Smad3-p27/p21 in BRL-3A cells

The liver has the powerful capacity to regenerate after injury or resection. In one of our previous studies, GPR50 was observed to be significantly upregulated at 6 h, following a partial hepatectomy (PH) in rat liver regeneration (LR) via gene expression profile. However, little research has been done on the regulation and mechanism of GPR50 in the liver. Herein, we observed that the overexpression of GPR50 inhibited the proliferation of BRL-3A cells. To further explore the molecular mechanisms of GPR50 in the regulation of BRL-3A cell proliferation, interaction between GPR50 and transforming growth factor-beta I (TβRI) and iTRAQ^TM differential proteomic analysis were elucidated, which suggested that GPR50 may interact with TβRI to activate the TGF-β signaling pathway and arrest BRL-3A cell cycle G1/S transition. Subsequently, the potential mechanism underlying the role of GPR50 in hepatocyte growth was also explored through the addition of a signaling pathway inhibitor. These data suggested that interaction between the orphan GPR50 receptor and TβRI induced the G1⁄S-phase cell cycle arrest of BRL-3A cells via the Smad3-p27/p21 pathway.

The Crosstalk between Autophagy and Apoptosis Is Necessary for Myogenic Differentiation

Skeletal muscle is a major organ in animals, which constitutes over 40% of livestock body weight, and plays a critical role in metabolism and homeostasis in an organism. Autophagy and apoptosis are two major processes to determine cell fate. Recently, the importance of autophagy and apoptosis in myogenesis has been identified; however, their crosstalk is not well defined. In this study, we aimed to explore the relationship between apoptosis and autophagy during myogenic differentiation. The results showed that the level of autophagy was consistent with apoptosis during myogenic differentiation. The increased apoptosis activated autophagy, and then autophagy inhibited apoptosis in turn to prevent excessive apoptosis and maintain the stability of cells. The interaction between autophagy and apoptosis determines the balance of cell death and cell survival, allowing the skeletal muscle cells to differentiate normally.

Unlike Its Paralog LEDGF/p75, HRP-2 Is Dispensable for MLL-R Leukemogenesis but Important for Leukemic Cell Survival

HDGF-related protein 2 (HRP-2) is a member of the Hepatoma-Derived Growth Factor-related protein family that harbors the structured PWWP and Integrase Binding Domain, known to associate with methylated histone tails or cellular and viral proteins, respectively. Interestingly, HRP-2 is a paralog of Lens Epithelium Derived Growth Factor p75 (LEDGF/p75), which is essential for MLL-rearranged (MLL-r) leukemia but dispensable for hematopoiesis. Sequel to these findings, we investigated the role of HRP-2 in hematopoiesis and MLL-r leukemia. Protein interactions were investigated by co-immunoprecipitation and validated using recombinant proteins in NMR. A systemic knockout mouse model was used to study normal hematopoiesis and MLL-ENL transformation upon the different HRP-2 genotypes. The role of HRP-2 in MLL-r and other leukemic, human cell lines was evaluated by lentiviral-mediated miRNA targeting HRP-2. We demonstrate that MLL and HRP-2 interact through a conserved interface, although this interaction proved less dependent on menin than the MLL-LEDGF/p75 interaction. The systemic HRP-2 knockout mice only revealed an increase in neutrophils in the peripheral blood, whereas the depletion of HRP-2 in leukemic cell lines and transformed primary murine cells resulted in reduced colony formation independently of MLL-rearrangements. In contrast, primary murine HRP-2 knockout cells were efficiently transformed by the MLL-ENL fusion, indicating that HRP-2, unlike LEDGF/p75, is dispensable for the transformation of MLL-ENL leukemogenesis but important for leukemic cell survival.

Integrated miRNA-mRNA transcriptomic analysis reveals epigenetic-mediated embryonic muscle growth differences between Wuzhishan and Landrace pigs1

Pig is one of the major dietary protein sources for human consumption, from which muscle is the largest protein origin. However, molecular mechanisms concerning early porcine embryonic muscle development distinctions between pig breeds are still unclear. In this study, an integrated analysis of transcriptome and miRNAome was conducted using longissimus dorsi muscle of 4 early embryonic stages around the primary myofiber formation time (18-, 21-, 28-, and 35-d post coitus) from 2 pig breeds (Landrace [LR] and Wuzhishan [WZS]) differing in meat mass. The global miRNA/mRNA expression profile showed that WZS prepared for myogenic developmental processes earlier than LR. After identifying and analyzing the interaction network of top 100 up-/down-regulated miRNA and their target genes, we were able to find 3 gene clusters: chromatin modification-related (Chd2, H3f3a, Chd6, and Mll1), myogenesis-related (Pax3, Pbx1, Mef2a, and Znf423), and myosin component-related (Mylk, Myo5a, Mylk4, Myh9, and Mylk2) gene clusters. These genes may involve in miRNA-gene myogenic regulatory network that plays vital role in regulating distinct early porcine embryonic myogenic processes between LR and WZS. In summary, our study reveals an epigenetic-mediated myogenic regulatory axial that will help us to decipher molecular mechanisms concerning early porcine embryonic muscle development distinctions between pig breeds.

The Effects of Maternal Obesity on Porcine Placental Efficiency and Proteome

Maternal obesity is associated with impaired maternal metabolism and affects the developmental programming of the fetus. The placenta is dysfunctional when exposed to an obese intrauterine environment and can transduce and mediate detrimental maternal impacts to the fetus through mechanisms that remain largely unknown. The main objective of this study was to investigate the effects of maternal obesity on the porcine placental proteome and to analyze the deregulated proteins and potential pathways predicted to be disturbed in obese placentas, using sows with high backfat as a model of obese pregnancy. The sows were divided into two groups based on their backfat thickness: normal backfat (NBF, 17-22 mm; n = 30) and high backfat (HBF, ≥23 mm; n = 30) as the maternal obesity group. The placental tissues used for the proteomic and biochemical analyses were obtained through vaginal delivery, and the maternal blood samples used to determine the metabolic parameters were collected at day 107 of pregnancy. Our study demonstrated that HBF sows had significantly decreased placental efficiency, increased plasma-free fatty acids and triglyceride levels, and increased proinflammatory cytokines plasma levels (p < 0.05). HBF placentas had significantly higher malondialdehyde level, lower total antioxidant capacity and antioxidase activity, increased triglyceride content and enhanced proinflammatory tumor necrosis factor- α (TNF-α) and interleukin-6 (IL-6) contents (p < 0.05). Among the 4652 proteins identified using the proteomic method, 343 were quantified as differentially abundant proteins, which were involved in many vital biological processes. Based on our bioinformatic and placental biochemical analyses, we concluded that maternal obesity is associated with abnormal carbohydrate and lipid metabolism, mitochondrial dysfunction, decreased steroid hormone biosynthesis, and increased oxidative stress and inflammation in the placenta. The results of this study are undoubtedly valuable to other researchers.

Earlier demethylation of myogenic genes contributes to embryonic precocious terminal differentiation of myoblasts in miniature pigs

Here, we performed whole-genome bisulfite sequencing of longissimus dorsi muscle from Landrace and Wuzhishan (WZS) miniature pigs during 18, 21, and 28 d postcoitum. It was uncovered that in regulatory regions only around transcription start sites (TSSs), gene expression and methylation showed negative correlation, whereas in gene bodies, positive correlation occurred. Furthermore, earlier myogenic gene demethylation around TSSs and earlier hypermethylation of myogenic genes in gene bodies were considered to trigger their earlier expression in miniature pigs. Furthermore, by analyzing the methylation pattern of the myogenic differentiation 1(MyoD) promoter and distal enhancer, we found that earlier demethylation of the MyoD distal enhancer in WZSs contributes to its earlier expression. Moreover, DNA demethylase Tet1 was found to be involved in the demethylation of the myogenin promoter and promoted immortalized mouse myoblast cell line (C2C12) and porcine embryonic myogenic cell differentiation. This study reveals that earlier demethylation of myogenic genes contributes to precocious terminal differentiation of myoblasts in miniature pigs.-Zhang, X., Nie, Y., Cai, S., Ding, S., Fu, B., Wei, H., Chen, L., Liu, X., Liu, M., Yuan, R., Qiu, B., He, Z., Cong, P., Chen, Y., Mo, D. Earlier demethylation of myogenic genes contributes to embryonic precocious terminal differentiation of myoblasts in miniature pigs.

A comparison of prenatal muscle transcriptome and proteome profiles between pigs with divergent growth phenotypes

The growth of pigs is an important economic trait that involves multiple genes and coordinated regulatory mechanisms. The growth rate and potential of skeletal muscles are largely decided by embryonic myofiber development. Tibetan pig (TP) that is a mini-type breed has a divergent phenotype in growth rate and adult body weight with Wujin pig (WJ) and large White pig (LW). In the current study, the transcriptome (using RNA-seq) and proteome (using the isobaric tag for relative and absolute quantification [iTRAQ]) data from the prenatal muscle tissues were analyzed to identify the genes related to postnatal growth rate and growth potential in pigs. In the RNA-seq experiment, 19 626 genes were detected in the embryonic muscle tissues, and 3626 unique differentially expressed genes (DEGs) were identified in TP in comparison to that in LW and WJ. In the iTRAQ experiment, 2474 proteins were detected, and 735 unique differentially expressed proteins (DEPs) were identified in TP in comparison to that in LW and WJ. Combining the DEGs and DEPs, 209 genes were found to be differentially expressed, consistently at both the messenger RNA and protein levels, between TP and the other two breeds; these are mainly involved in 2-oxocarboxylic acid metabolism, citrate cycle, and biosynthesis of amino acids. Of these, 20 genes that were related to myoblast differentiation and muscle fiber formation might have important roles in determining the postnatal growth rate and potential body weight in pigs. Our results provide new candidate genes and insights into the molecular mechanisms involved muscle growth traits in pigs.

Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics

BACKGROUND

Scallops possess striated and catch adductor muscles, which have different structure and contractile properties. The striated muscle contracts very quickly for swimming, whereas the smooth catch muscle can keep the shells closed for long periods with little expenditure of energy. In this study, we performed proteomic and transcriptomic analyses of differences between the striated (fast) and catch (slow) adductor muscles in Yesso scallop Patinopecten yessoensis.

RESULTS

Transcriptomic analysis reveals 1316 upregulated and 8239 downregulated genes in slow compared to fast adductor muscle. For the same comparison, iTRAQ-based proteomics reveals 474 differentially expressed proteins (DEPs), 198 up- and 276 downregulated. These DEPs mainly comprise muscle-specific proteins of the sarcoplasmic reticulum, extracellular matrix, and metabolic pathways. A group of conventional muscle proteins-myosin heavy chain, myosin regulatory light chain, myosin essential light chain, and troponin-are enriched in fast muscle. In contrast, paramyosin, twitchin, and catchin are preferentially expressed in slow muscle. The association analysis of proteomic and transcriptomic data provides the evidences of regulatory events at the transcriptional and posttranscriptional levels in fast and slow muscles. Among 1236 differentially expressed unigenes, 22.7% show a similar regulation of mRNA levels and protein abundances. In contrast, more unigenes (53.2%) exhibit striking differences between gene expression and protein abundances in the two muscles, which indicates the existence of fiber-type specific, posttranscriptional regulatory events in most of myofibrillar proteins, such as myosin heavy chain, titin, troponin, and twitchin.

CONCLUSIONS

This first, global view of protein and mRNA expression levels in scallop fast and slow muscles reveal that regulatory mechanisms at the transcriptional and posttranscriptional levels are essential in the maintenance of muscle structure and function. The existence of fiber-type specific, posttranscriptional regulatory mechanisms in myofibrillar proteins will greatly improve our understanding of the molecular basis of muscle contraction and its regulation in non-model invertebrates.

Proteomic and microRNA Transcriptome Analysis revealed the microRNA-SmyD1 network regulation in Skeletal Muscle Fibers performance of Chinese perch

Fish myotomes are comprised of anatomically segregated fast and slow muscle fibers that possess different metabolic and contractile properties. Although the expression profile properties in fast and slow muscle fibers had been investigated at the mRNA levels, a comprehensive analysis at proteomic and microRNA transcriptomic levels is limited. In the present study, we first systematically compared the proteomic and microRNA transcriptome of the slow and fast muscles of Chinese perch (Siniperca chuatsi). Total of 2102 proteins were identified in muscle tissues. Among them, 99 proteins were differentially up-regulated and 400 were down-regulated in the fast muscle compared with slow muscle. MiRNA microarrays revealed that 199 miRNAs identified in the two types of muscle fibers. Compared with the fast muscle, the 32 miRNAs was up-regulated and 27 down-regulated in the slow muscle. Specifically, expression of miR-103 and miR-144 was negatively correlated with SmyD1a and SmyD1b expression in fast and slow muscles, respectively. The luciferase reporter assay further verified that the miR-103 and miR-144 directly regulated the SmyD1a and SmyD1b expression by targeting their 3′-UTR. The constructed miRNA-SmyD1 interaction network might play an important role in controlling the development and performance of different muscle fiber types in Chinese perch.

iTRAQ-Based Proteomics Analysis and Network Integration for Kernel Tissue Development in Maize

Grain weight is one of the most important yield components and a developmentally complex structure comprised of two major compartments (endosperm and pericarp) in maize (Zea mays L.), however, very little is known concerning the coordinated accumulation of the numerous proteins involved. Herein, we used isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative proteomic method to analyze the characteristics of dynamic proteomics for endosperm and pericarp during grain development. Totally, 9539 proteins were identified for both components at four development stages, among which 1401 proteins were non-redundant, 232 proteins were specific in pericarp and 153 proteins were specific in endosperm. A functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the tissue development. Three and 76 proteins involved in 49 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were integrated for the specific endosperm and pericarp proteins, respectively, reflecting their complex metabolic interactions. In addition, four proteins with important functions and different expression levels were chosen for gene cloning and expression analysis. Different concordance between mRNA level and the protein abundance was observed across different proteins, stages, and tissues as in previous research. These results could provide useful message for understanding the developmental mechanisms in grain development in maize.

An integrated analysis revealed different microRNA-mRNA profiles during skeletal muscle development between Landrace and Lantang pigs

Pigs supply vital dietary proteins for human consumption, and their economic value depends largely on muscle production. MicroRNAs are known to play important roles in skeletal muscle development. However, their relationship to distinct muscle production between pig breeds remains unknown. Here, we performed an integrated analysis of microRNA-mRNA expression profiles for Landrace (LR, lean) pigs and the Chinese indigenous Lantang pig (LT, lard-type) during 8 stages of skeletal muscle developmental, including at 35, 49, 63, 77 dpc (days post coitum) and 2, 28, 90, 180 dpn (days postnatal). As differentially expressed-miRNA expression profiles can be well classified into two clusters by PCA analysis, we grouped the embryonic stages as G1 and the postnatal stages as G2. A total of 203 genes were predicted miRNA targets, and a STEM analysis showed distinct expression patterns between G1 and G2 in both breeds based on their transcriptomic data. Furthermore, a STRING analysis predicted interactions between 22 genes and 35 miRNAs, including some crucial myogenic factors and myofibrillar genes. Thus, it can be reasonably speculated that myogenic miRNAs may regulate myofibrillar genes in myofiber formation during embryonic stages and muscle hypertrophy during postnatal stages, leading to distinct differences in muscle production between breeds.

Proteomic Analysis of Chicken Skeletal Muscle during Embryonic Development

Embryonic growth and development of skeletal muscle is a major determinant of muscle mass, and has a significant effect on meat production in chicken. To assess the protein expression profiles during embryonic skeletal muscle development, we performed a proteomics analysis using isobaric tags for relative and absolute quantification (iTRAQ) in leg muscle tissues of female Xinghua chicken at embryonic age (E) 11, E16, and 1-day post hatch (D1). We identified 3,240 proteins in chicken embryonic muscle and 491 of them were differentially expressed (fold change ≥ 1.5 or ≤ 0.666 and p < 0.05). There were 19 up- and 32 down-regulated proteins in E11 vs. E16 group, 238 up- and 227 down-regulated proteins in E11 vs. D1 group, and 13 up- and 5 down-regulated proteins in E16 vs. D1 group. Protein interaction network analyses indicated that these differentially expressed proteins were mainly involved in the pathway of protein synthesis, muscle contraction, and oxidative phosphorylation. Integrative analysis of proteome and our previous transcriptome data found 189 differentially expressed proteins that correlated with their mRNA level. The interactions between these proteins were also involved in muscle contraction and oxidative phosphorylation pathways. The lncRNA-protein interaction network found four proteins DMD, MYL3, TNNI2, and TNNT3 that are all involved in muscle contraction and may be lncRNA regulated. These results provide several candidate genes for further investigation into the molecular mechanisms of chicken embryonic muscle development, and enable us to better understanding their regulation networks and biochemical pathways.

iTRAQ-based proteomic analysis reveals key proteins affecting muscle growth and lipid deposition in pigs

Growth rate and meat quality, two economically important traits in pigs, are controlled by multiple genes and biological pathways. In the present study, we performed a proteomic analysis of longissimus dorsi muscle from six-month-old pigs from two Chinese native mini-type breeds (TP and DSP) and two introduced western breeds (YY and LL) using isobaric tag for relative and absolute quantification (iTRAQ). In total, 4,815 peptides corresponding to 969 proteins were detected. Comparison of expression patterns between TP-DSP and YY-LL revealed 288 differentially expressed proteins (DEPs), of which 169 were up-regulated and 119 were down-regulated. Functional annotation suggested that 28 DEPs were related to muscle growth and 15 to lipid deposition. Protein interaction network predictions indicated that differences in muscle growth and muscle fibre between TP-DSP and YY-LL groups were regulated by ALDOC, ENO3, PGK1, PGK2, TNNT1, TNNT3, TPM1, TPM2, TPM3, MYL3, MYH4, and TNNC2, whereas differences in lipid deposition ability were regulated by LPL, APOA1, APOC3, ACADM, FABP3, ACADVL, ACAA2, ACAT1, HADH, and PECI. Twelve DEPs were analysed using parallel reaction monitoring to confirm the reliability of the iTRAQ analysis. Our findings provide new insights into key proteins involved in muscle growth and lipid deposition in the pig.