Identification of Key Genes Associated With Early Calf-Hood Nutrition in Subcutaneous and Visceral Adipose Tissues by Co-Expression Analysis

Pan, Cuili; Yang, Chaoyun; Ma, Yanfen; Sheng, Hui; Lei, Zhaoxiong; Wang, Shuzhe; Hu, Honghong; Xue, Feng; Zhang, Junxing; Ma, Yun

doi:10.3389/fvets.2022.831129

Cited by 2 publications

(1 citation statement)

References 51 publications

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“…Among these, circRNA 21:6969877|69753491 has been shown to be involved in lipid metabolism in a previous study, therefore it likely affects fat deposition. Gene significance (GS>0.8) ( 37 , 38 ) and module membership (MM>0.8) ( 37 – 39 ) values showed a high correlation between circRNA 21:6969877|69753491 and two traits (month and weight) of buffalo Figure 1F .…”

Section: Resultsmentioning

confidence: 99%

Weighted Gene Co-expression Network Analysis Revealed That CircMARK3 Is a Potential CircRNA Affects Fat Deposition in Buffalo

Xue

Jian-Gao

et al. 2022

Front. Vet. Sci.

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BackgroundBuffalo meat is increasingly widely accepted for consumption as it shares several quality attributes with cattle meat (beef). Hence, there is a huge opportunity for growth in the buffalo meat industry. However, buffalo meat has relatively low intramuscular fat (IMF) content, affecting its flavor, tenderness and juiciness. As there is a dearth of information on factors that control fat deposition, this study was undertaken to provide new candidate factor associated with buffalo fat deposition. Circular RNA (circRNA) is a novel class of non-coding RNA with a closed-loop structure, and play an important role in fat deposition.MethodsIn this study, weighted gene co-expression network analysis (WGCNA) was used to construct a circRNA co-expression network and revealed a candidate circRNA that may affect the IMF deposition of buffalo as determined by RT-qPCR, semiquantitative PCR and gain-of-function experiments.ResultsHerein, WGCNA determined that one module (turquoise module) is significantly associated with the growth and development stages of buffalo. Further analysis revealed a total of 191 overlapping circRNAs among differentially expressed (DE) circRNAs and the co-expression module. A candidate circRNA was found, 21:6969877|69753491 (circRNA_ID), with a reported involvement in lipid metabolism. This circRNA is stably expressed and originates from the MARK3 gene, hence the name circMARK3. circMARK3 is highly expressed in adipose tissue and mature adipocytes and is located in the cytoplasm. Gain-of-function experiments demonstrated that circMARK3 promoted adipogenic differentiation of buffalo adipocytes and 3T3-L1 cells by up-regulating the expression levels of adipogenic marker genes PPARG, C/EBPα and FABP4.ConclusionThese results indicate that circMARK3 is a potential factor that promotes fat deposition by regulating adipocyte differentiation and adipogenesis in buffalo.

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Section: Resultsmentioning

confidence: 99%

Weighted Gene Co-expression Network Analysis Revealed That CircMARK3 Is a Potential CircRNA Affects Fat Deposition in Buffalo

Xue

Jian-Gao

et al. 2022

Front. Vet. Sci.

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Transcriptome-wide mapping of milk somatic cells upon subclinical mastitis infection in dairy cattle

Bisutti

Mach

Giannuzzi

et al. 2023

J Animal Sci Biotechnol

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Background Subclinical intramammary infection (IMI) represents a significant problem in maintaining dairy cows’ health. Disease severity and extent depend on the interaction between the causative agent, environment, and host. To investigate the molecular mechanisms behind the host immune response, we used RNA-Seq for the milk somatic cells (SC) transcriptome profiling in healthy cows (n = 9), and cows naturally affected by subclinical IMI from Prototheca spp. (n = 11) and Streptococcus agalactiae (S. agalactiae; n = 11). Data Integration Analysis for Biomarker discovery using Latent Components (DIABLO) was used to integrate transcriptomic data and host phenotypic traits related to milk composition, SC composition, and udder health to identify hub variables for subclinical IMI detection. Results A total of 1,682 and 2,427 differentially expressed genes (DEGs) were identified when comparing Prototheca spp. and S. agalactiae to healthy animals, respectively. Pathogen-specific pathway analyses evidenced that Prototheca’s infection upregulated antigen processing and lymphocyte proliferation pathways while S. agalactiae induced a reduction of energy-related pathways like the tricarboxylic acid cycle, and carbohydrate and lipid metabolism. The integrative analysis of commonly shared DEGs between the two pathogens (n = 681) referred to the core-mastitis response genes, and phenotypic data evidenced a strong covariation between those genes and the flow cytometry immune cells (r2 = 0.72), followed by the udder health (r2 = 0.64) and milk quality parameters (r2 = 0.64). Variables with r ≥ 0.90 were used to build a network in which the top 20 hub variables were identified with the Cytoscape cytohubba plug-in. The genes in common between DIABLO and cytohubba (n = 10) were submitted to a ROC analysis which showed they had excellent predictive performances in terms of discriminating healthy and mastitis-affected animals (sensitivity > 0.89, specificity > 0.81, accuracy > 0.87, and precision > 0.69). Among these genes, CIITA could play a key role in regulating the animals’ response to subclinical IMI. Conclusions Despite some differences in the enriched pathways, the two mastitis-causing pathogens seemed to induce a shared host immune-transcriptomic response. The hub variables identified with the integrative approach might be included in screening and diagnostic tools for subclinical IMI detection.

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Identification of Key Genes Associated With Early Calf-Hood Nutrition in Subcutaneous and Visceral Adipose Tissues by Co-Expression Analysis

Cited by 2 publications

References 51 publications

Weighted Gene Co-expression Network Analysis Revealed That CircMARK3 Is a Potential CircRNA Affects Fat Deposition in Buffalo

Weighted Gene Co-expression Network Analysis Revealed That CircMARK3 Is a Potential CircRNA Affects Fat Deposition in Buffalo

Transcriptome-wide mapping of milk somatic cells upon subclinical mastitis infection in dairy cattle

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