To date, several transcriptome-based studies have been conducted to identify DEGs related to fat-tail formation through comparison of fat- and thin-tailed sheep breeds (Table 1). However, one of the main problems of these studies is a small number of biological replicates due to the cost of sequencing, which can lead to decrease the statistical power to detect DEGs. In this regard, the variation among the identified DEGs by different datasets (Fig. 2) emphasized the importance of meta-analysis to obtain core genes that are consistently DEGs across multiple studies. Some of the lack of agreement from one study to another can be attributed to differences in the experimental conditions such as environmental variables, bioinformatics pipeline, etc.
It should be noted that various sheep breeds have been used in the six studies, however these breeds can be used to identify core genes involved in fat deposition in the fat-tail of sheep. While vertebrate species differ in many phenotypic traits, however, organ physiology in mammals are conserved. Furthermore, it is well known that many biological processes and pathways are deeply conserved among the species30. Based on this idea that many developmental gene expression patterns are conserved across mammals, rodents can be applied as models of human tissues physiology31. Previous studies in this area have shown that inter-study distances between similar tissues of various species were generally less than intra-study distances among various tissues, implying that meta-analysis of different RNA-seq studies can provide insights into the molecular mechanisms behind the mammalian tissues32. Here, a meta-analysis was performed to find the common core DEGs across six studies and remove the inconsistencies in these datasets to obtain a deeper biological insight associated with fat deposition in tail of sheep, compared to that achieved through single dataset. These core genes can be considered as putative candidates involved in fat-tail development regardless of the different characteristics of the studies. Therefore, our aim was to shed light into the molecular mechanisms conserved across the sheep breeds instead of identifying specific mechanisms in each breed.
To better integrate the datasets, a standard and similar bioinformatics workflow was applied to analyze the raw RNA-Seq data from the studies, in which different pipelines were used. To further evaluate the consistency of the DEGs across the datasets, Jackknife sensitivity analysis was applied and revealed that most of the DEGs (> 80%) passed at least 50% of the Jackknife tests, which indicates the robustness of the results and independency of these genes to a single study. It is worth to note that in this study only DEGs with the same pattern of expression over most of the datasets (> 50%) were considered, which make them more robust and constitutes a suitable way for better understanding the regulatory mechanisms of fat-tail development. To assess potential functions of DEGs in fat-tail development, we investigate their relationships with the QTLs related to sheep fatness and found that they were significantly enriched in these QTLs. These findings reinforced that the identified DEGs may play important roles in fat-tail development in sheep.
GO terms as well as KEGG pathways associated with fat metabolism were the most enriched terms in the DEGs, which explains the fact that these genes can be related to fat-tail formation (Supplementary File S3). Some of the DEGs grouped under terms that were directly or indirectly related to fat metabolism, including LEPRRBP4, CSNK2B, EPHX1, SCD, ALOX15, SCD5, HSPA6, ACLY, ELOVL6, FOXO3, PPP5C, DAGLA, ACSF2, DHCR24, JUNB, FNDC5, FMO2, FOS, FRZB, ZBTB16, LSS, COL5A1, SLC27A2, SPTLC3, PLPP3, ZBTB20, SMPDL3B, LBP, LPIN1, IL6, PDGFRA, CCL21, SPP1, PAI-1, HSD11B1, MTMR4, S100A1, COL6A3, TNNC2, ITGA1, SCG5, NR4A1, DUSP1 and APOE5,7–13,33-36. Most of these genes passed at least 50% of the Jackknife tests or reside in the QTLs previously found to be linked to sheep fatness (Supplementary File s S2 and S4). Some of these genes require particular attention considering that they have been previously linked to fat deposition.
PPIs network construction by STRING database confirmed that up- and down-regulated DEGs were members of functional interaction networks. It is well known that genes from the same sub-network in a PPI network more probably play similar roles and are implicated in the same biological functions. To investigate this hypothesis, sub-network analysis on the PPI network results was performed and two of the three identified sub-networks in the down-regulated DEGs were significantly enriched in different GO terms and KEGG pathways. Hence, it might be possible to hypothesize that genes of green sub-network may be involved in fat deposition in tail of sheep breeds, as “Biosynthesis of unsaturated fatty acids” and “Lipid biosynthetic process” were significantly enriched (Fig. 5). Some genes of this sub-network that may be of particular interests are SCD, SCD5, ELOVL6, ACLY, DHCR24, SPTLC3, LSS, LPIN1, SLC27A2, CKAP2, FOS, JUNB, FOXO3, EBF2 and MYBL2, which are located in the fatness-related QTLs regions or passed at least 50% of the Jackknife tests (Supplementary File s S2 and S4). In our previous study we hypothesized that down-regulation of the related genes to lipid metabolism in fa-tailed breed may be associated with other pathways than fat deposition such as fat composition5 or fatty acid oxidation. It has been demonstrated that the breed has significant effect on fatty acid composition of tail fat37. Here, the similar results were obtained as some members of green sub-network were involved in the pathways associated with fat composition or fatty acid oxidation such as SCD, SCD5, ELOVL6, ACLY, SLC27A2 and LPIN1.
Isoforms of stearoyl CoA desaturase (SCD and SCD5) play important roles in desaturation of saturated fatty acids. Lower expression of these genes has been previously reported in fat-tailed than thin-tailed sheep breeds10,12, which can cause lower content of saturated fatty acids in fat-tailed breeds. In chicken, SCD5 expression was significantly correlated with levels of stearidonic acid38, which might lead to suppress adipocyte differentiation39. Very long-chain fatty acids protein 6 (ELOVL6) is well known as a major regulator of fatty acid composition in mammals40. The first step of de novo lipogenesis, the conversion of citrate into acetyl-CoA, is catalyzed by ACLY. This product, acetyl-CoA, can then be used as building block for long chain fatty acids, cholesterol synthesis and/or histone acetylation41. It has been shown that ACLY-deficient adipocytes accumulate lipid in vivo and display some differences in fatty acid content and synthesis42. Mammals express three lipin genes (LPIN1-3) that their functions are evolutionarily conserved. One of the important roles of these genes is transcriptional co-regulators of gene expression in the nucleus to promote fatty acid oxidation43. In accordance with our results, it was reported that the role of LPIN1 might be closely associated with fatty acid oxidation in the bovine liver44. Solute carrier family 27 member 2 (SLC27A2) is a transmembrane transporter coenzyme that participates in the long-chain fatty acid beta-oxidation45 as well as plays a key role in fatty acid degradation46. SLC27A2 was identified to be closely associated with tail phenotype in Zhang et al. study that investigated the transcriptome profiles of fat deposition in tail of sheep36. A recent study investigated the correlation of slow-growing meat type chicken liver gene expression with abdominal fat deposition using a time-course transcriptomic study (from the embryonic to the egg-producing period) and reported CKAP2 as one of the important candidates involved in fat metabolism47. Furthermore, in green sub-network, five genes including JUNB, FOXO3, EBF2, FOS and MYBL2 were transcription factors with known roles in lipid metabolism, which can be considered as regulators of this sub-network. A genome-wide association study showed that MYBL2 may be involved in abdominal fat deposition in chickens48. JUNB is a transcription factor whose role in lipid metabolism and fat cell differentiation has been documented49. Important roles of FOXO protein family in energy homeostasis and lipid metabolism have been highlighted in previous studies50. Based on our findings, lower expression of members of the green sub-network in fat-tailed sheep breeds are reasonable and might be potential candidate contributing to shaping fat-tail phenotype through regulating fat composition or fatty acid oxidation.
On the other hand, some pathways related to the fat metabolism including “Extracellular matrix (ECM)-receptor interaction”, “Focal adhesion” and “PI3K-Akt signaling pathway” were significantly enriched in the pink sub-network, which can further contribute to understanding the fat-tail development in sheep (Fig. 6). All the genes associated with these pathways (SPP1, COL1A1, ITGA2, ITGA1, VEGFA, COL6A6, COL4A6, PDGFRA, COL6A3, SDC1) were located in the QTLs related to fatness or passed at least 50% of the Jackknife tests (Supplementary File s S2 and S4), which indicated their potential involvement in fat-tail morphogenesis. Focal adhesion is related to ECM and act as mechanical linkages to the extracellular matrix51. Hence, the DEGs belonging to these two pathways were very similar (Supplementary File S3). ECM is essential for tissue homeostasis and consists of a complex mixture of functional macromolecules in adipose tissue, such as glycosaminoglycans, collagen, elastin, fibronectin, and lammin52. The ECM communicates with cells through cell surface-related elements such as integrin and regulates cell activities such as differentiation, proliferation, migration, adhesion and apoptosis53. ECM receptor interaction signaling pathway has been reported as a significant enriched pathway in the DEGs between fat- and thin-tailed sheep breeds in several previous studies5,10,15 as well as in the DEGs between lean and obese human54. Moreover, interaction between ECM components and transmembrane receptors of fat cells have been demonstrated to be associated with depot-specific adipogenesis in bovine55. However, we believed that research studies in animal filed have paid no sufficient attention to investigate the role of the ECM receptor interaction pathway in fat metabolism as well as fat-tail formation in sheep. ECM was detected as an inhibited KEGG pathway during differentiation of human mesenchymal stromal-cells into adipocytes. Down-regulated genes belonging to this pathway were in agreement with our results like collagen subunits IV, V and VI (COL1A1, COL6A6, COL4A6, and COL6A3), different integrins 1 and 2 (ITGA1 and ITGA2) and proteoglycans like syndecan 1 and 4 (SDC1). Down-regulation of these genes are attributed to cytoskeleton reorganization during adipogenesis56. Collagen type IV denaturation is reported to be associated with adipogenic differentiation57. In a comprehensive assessment to study the role of COL6A3 in human obesity and diabetes, it was revealed that COL6A3 expression increased after weight loss and showed a negative correlation with obesity, which is in good agreement with our findings in the current study58. Moreover, it has been shown that integrin α5 is down-regulated during adipogenesis in 3T3-L1 cells. Therefore, up regulation of this gene inhibits cellular differentiation59. Accordingly, our findings let hypothesize that ECM might mediates a mechanism involved in the differentiation of fat-tail adipocytes and lipid metabolism, thereby changing the fat-tail morphology of various sheep breeds.
Phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling pathway, as the other enriched pathway in pink sub-network, is a key pathway that specifically phosphorylates phosphatidylinositol, generate an intracellular second messengers and mediates glucose and lipid metabolism60. It is reported that PI3K/AKT signaling pathway has different functions in various adipocytes, as promote and inhibit the proliferation/differentiation in human adipocytes and 3T3-L1, respectively61,62. It has been shown that inhibition of this pathway in children with simple obesity participates in the occurrence and progression of obesity63. In a recent study, PI3K/AKT signaling pathways was enriched in the target genes of differentially expressed miRNAs between fat- and thin-tailed sheep breeds64 and suggested to be involved in biological processes related to fat deposition in fat-tail tissue. In the current study, enrichment of this pathway in the down-regulated genes in fat-tailed breeds suggesting that it may inhibits the proliferation and differentiation of lipid metabolism in fat-tail tissue and leads to differences in fat deposition between the different sheep breeds. Some of the DEGs belonging to PI3K/AKT signaling pathway in this study were included SPP1, PDGFRA, VEGFA and TNC. Positive and negative effects of SPP1 in fat deposition had been demonstrated in previous reports. Studies have established that this gene is synthesized by adipocytes and its higher expression is related to fat deposition65. In contrast, it is reported that interaction of SPP1 with integrin αv/β1 inhibits the adipogenesis of mesenchymal stem cells66. In agreement with our results, a recent study found that SPP1 negatively regulated adipogenic differentiation of peripheral blood-derived mesenchymal stem cells and interaction between novel-miR-659 and SPP1 coregulate fat deposition in castrated male pigs34. All these findings support the potential function of PI3K/AKT signaling pathway and its related genes in mediating lipolysis and energy expenditure, which can be led to lower fat deposition.
Some of the up-regulated DEGs in this study have been previously reported as candidate genes involved in fat-tail/fatness development or as DEG associated with fat metabolism in animal. Moreover, they were found in the fatness-related QTLs or passed at least 50% of the Jackknife tests (Supplementary File s S2 and S4). Some of the most important genes in light blue sub-network (Fig. 4) were IL6, RBP4, LEPR, PAI-1, CSNK2B and MTMR4. Recent studies highlighted the role of interleukins in lipid metabolism44. Interleukin-6 (IL-6) is known as a key regulator of adipose homeostasis in obesity. It is worth to note that in Farhadi et al., study9 this gene was down-regulated in fat-tailed breed and they suggested it as a potential candidate gene in fat-tail formation. However, our analysis revealed that this gene was up-regulated in fat-tailed breed in all studies, except Farhadi et al., study9. In this regard, results of a study showed that expression of IL-6 in lymphedema (a morbid disease characterized by adipose deposition67) is associated with adipose deposition. Since, IL-6 was identified as a highly connected gene in light blue sub-network (Fig. 4), the other genes in this cluster are expected to be potential candidate genes in fat-tail formation. Interestingly, most of the connected genes with IL-6 were reported to be involved in fat deposition processes, which reinforce the importance of light blue sub-network in fat deposition. For example, retinol binding protein 4 (RBP4), which is a novel adipokine, is mainly secreted by adipocytes and is related to obesity. This gene contributes to systemic insulin resistance that can lead to fat deposition68. Leptin receptor (LEPR), as other gene in light blue sub-network that is also located in fatness-related QTLs regions, was reported as candidate gene affecting fat deposition in pig69. Higher levels of plasminogen activator inhibitor-1 (PAI-1) in plasma was reported to be a biochemical marker of obesity70. The association between PAI-1 and fat deposition had been well established in animal studies and the location of this gene in the QTLs linked to sheep fatness make it interesting for further functional investigations71.
EPHX1, HSD11B1, FMO2, S100A1 and HSPA6 were some of the important up-regulated genes in orange sub-network (Fig. 4). Association between EPHX1 and adipogenesis in mesenchymal stem cells through the activation of cryoprotective lipid mediators had been explained previously72. Rosu-Myles et al., reported that EPHX1 expressing cells in human stromal cultures can be led to increased numbers of cells that have committed to the adipocyte lineage73. FMO2 is a member of the FMO gene family and catalyze the NADPH-dependent oxidative metabolism of a wide array of foreign chemicals as well as is involved in fat deposition, adipogenesis and fatty acid biosynthesis11. FMO3, as other member of this family, was reported as important candidate in fat metabolism of sheep through inhibiting fatty acid oxidation13. Consistent with these observations, FMOs 1, 2, and 4 knockout mice exhibited a lean phenotype and stored less triglycerides in their white adipose tissue compared to wild-type mice, despite similar food intake74. HSD11B1 is well known to be closely related to the accumulation of abdominal fat75. Recently, an RNA-Seq study was performed to explore the effects of castration on fat deposition in different parts of pigs and HSD11B1 was reported as a factor affects glucose uptake by adipocytes and leads to obesity76. In Arora et al., study HSPA6 was reported as an important regulator of fatty acid metabolism in the skeletal muscles of sheep33. Adipogenesis regulatory factor (ADIRF), as other important up-regulated gene, promotes adipocyte differentiation by enhancing the expression of peroxisome proliferator-activated receptor gamma (PPARG) and CCAAT-enhancer-binding protein alpha (CEBPA) in 3T3 L1 cells and play an important role in fat cell development. Higher expression of this gene in obese individuals, suggesting a role for ADIRF in the development of obesity77. Angiopoietin-like 8 (ANGPTL8) exhibits its effects by inducing insulin receptor to inhibits lipolysis and controls post-prandial fat storage in white adipose tissue. This gene directs fatty acids to adipose tissue for storage during the fed state. Serpin family E member 1 (SERPINE1) was highly expressed in obese individuals and demonstrated as a key gene associated with the network pathway analysis of obesity78. Altogether, these results support the potential role of up-regulated genes, especially light blue and orange sub-networks in fat deposition in tail of sheep.
Totally, 170 unique DEGs (77 up- and 93 down-regulated) were found in meta-analysis that were not identified as DEGs in individual studies (Fig. 2), which can be attributed to the more statistical power of meta-analysis than individual studies for identifying new candidate genes associated with fat-tail formation. Of which, 38 DEGs (17 up and 21 down-regulated) were located in QTLs regions related to fatness of sheep, which further support that their functions might be relevant. Some of these genes have been previously reported to be related to lipid metabolism including NR4A1, ACSF2, MYC, SPP1, PLPP3, PHOSPHO1 and ACP6. For example, NR4A1 encodes a nuclear receptor (transcription factor) that is involved in regulation of lipid metabolism and modulating lipolysis in muscle35. It is reported that female NR4A1 deficient mice exhibited higher fat mass compared to wild-type mice, under the same high-fat diet79. This gene plays a vital role in the regulation of liver fat content35. Expression of NR4A1 is reported to be negatively correlated with body-fat content and insulin sensitivity, as its expression was significantly lower in the muscle of obese men in comparison to lean men80. MYC, which is a transcription factor, plays vital roles in lipid metabolism81. Furthermore, ACSF2 is involved in the acyl-CoA metabolic process and malonyl-CoA metabolic process in mammals as well as reported to be associated with avian lipid metabolism82,83. These findings suggested a link between differentially expressed of these genes and fat-tail development in sheep.