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For: Hao D, Wang X, Yang Y, Thomsen B, Holm LE, Qu K, Huang B, Chen H. Integrated Analysis of mRNA and MicroRNA Co-expressed Network for the Differentiation of Bovine Skeletal Muscle Cells After Polyphenol Resveratrol Treatment. Front Vet Sci 2022;8:777477. [PMID: 35036414 PMCID: PMC8759604 DOI: 10.3389/fvets.2021.777477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/15/2021] [Indexed: 01/01/2023] Open

For:	Hao D, Wang X, Yang Y, Thomsen B, Holm LE, Qu K, Huang B, Chen H. Integrated Analysis of mRNA and MicroRNA Co-expressed Network for the Differentiation of Bovine Skeletal Muscle Cells After Polyphenol Resveratrol Treatment. Front Vet Sci 2022;8:777477. [PMID: 35036414 PMCID: PMC8759604 DOI: 10.3389/fvets.2021.777477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/15/2021] [Indexed: 01/01/2023] Open

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Cited by Other Article(s)

Gong G, Fan Y, Yan X, Li W, Yan X, Liu H, Zhang L, Su Y, Zhang J, Jiang W, Liu Z, Wang Z, Wang R, Zhang Y, Lv Q, Li J, Su R. Identification of Genes Related to Hair Follicle Cycle Development in Inner Mongolia Cashmere Goat by WGCNA. Front Vet Sci 2022;9:894380. [PMID: 35774980 PMCID: PMC9237575 DOI: 10.3389/fvets.2022.894380] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open

Abstract Cashmere goat from Inner Mongolia is an excellent local breed in China, and the related cashmere product is a kind of precious textile raw material with high price. Cashmere is generated from secondary hair follicles, which has obvious annual periodicity and includes three different stages: anagen, catagen, and telogen. Therefore, we investigated skin transcriptome data for 12 months using weighted gene co-expression network analysis (WGCNA) to explore essential modules, pathways, and genes responsible for the periodic growth and development of secondary hair follicles. A total of 17 co-expression modules were discovered by WGCNA, and there is a strong correlation between steelblue module and month (0.65, p = 3E−09), anagen (0.52, p = 1E−05), telogen (−0.6, p = 8E−08). Gene expression was generally high during late anagen to catagen (June to December), while expression was downregulated from telogen to early anagen (January–May), which is similar to the growth rule of hair follicle cycle. KEGG pathway enrichment analyses of the genes of steelblue module indicated that genes are mainly enriched in Cell cycle, Wnt signaling pathway, p53 signaling pathway and other important signal pathways. These genes were also significantly enriched in GO functional annotation of the cell cycle, microtubule movement, microtubule binding, tubulin binding, and so on. Ten genes (WIF1, WNT11, BAMBI, FZD10, NKD1, LEF1, CCND3, E2F3, CDC6, and CDC25A) were selected from these modules, and further identified as candidate biomarkers to regulate periodic development of hair follicles using qRT-PCR. The Wnt signaling pathway and Cell cycle play an important role in the periodic development of hair follicles. Ten genes were identified as essential functional molecules related to periodic development of hair follicle. These findings laid a foundation for understanding molecular mechanisms in biological functions such as hair follicle development and hair growth in cashmere goats. Collapse

Affiliation(s)

Gao Gong College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Yixing Fan College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
Xiaochun Yan College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Wenze Li College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Xiaomin Yan College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Hongfu Liu College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Ludan Zhang College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Yixing Su College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Jiaxin Zhang College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Wei Jiang College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Zhihong Liu College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Zhiying Wang College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Ruijun Wang College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Yanjun Zhang College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
Qi Lv College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China Engineering Research Center for Goat Genetics and Breeding, Hohhot, China *Correspondence: Qi Lv
Jinquan Li College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China Engineering Research Center for Goat Genetics and Breeding, Hohhot, China Jinquan Li
Rui Su College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China Engineering Research Center for Goat Genetics and Breeding, Hohhot, China Rui Su

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Gong G, Fan Y, Li W, Yan X, Yan X, Zhang L, Wang N, Chen O, Zhang Y, Wang R, Liu Z, Jiang W, Li J, Wang Z, Lv Q, Su R. Identification of the Key Genes Associated with Different Hair Types in the Inner Mongolia Cashmere Goat. Animals (Basel) 2022;12:ani12111456. [PMID: 35681921 PMCID: PMC9179306 DOI: 10.3390/ani12111456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/10/2022] Open

Abstract

The Inner Mongolia cashmere goat is an excellent local breed in China. According to the characteristics of wool quilts, the Inner Mongolia cashmere goat can be divided into three types: a long-hair type (hair length of >22 cm), a short-hair type (hair length of ≤13 cm), and an intermediate type (hair length of >13 cm and ≤22 cm). It is found that hair length has a certain reference value for the indirect selection of other important economic traits of cashmere. In order to explore the molecular mechanisms and related regulatory genes of the different hair types, a weighted gene coexpression network analysis (WGCNA) was carried out on the gene expression data and phenotypic data of 12-month-old Inner Mongolia cashmere goats with a long-hair type (LHG) and a short-hair type (SHG) to explore the coexpression modules related to different coat types and nine candidate genes, and detect the relative expression of key candidate genes. The results showed that the WGCNA divided these genes into 19 coexpression modules and found that there was a strong correlation between one module and different hair types. The expression trends of this module’s genes were different in the two hair types, with high expression in the LHG and low expression in the SHG. GO functions are mainly concentrated in cellular components, including intermediate filaments (GO:0005882), intermediate filament cytoskeletons (GO:0045111), and cytoskeletal parts (GO:0044430). The KEGG pathway is mainly enriched in arginine as well as proline metabolism (chx00330) and the MAPK signaling pathway (chx04010). The candidate genes of the different hair types, including the KRT39, KRT74, LOC100861184, LOC102177231, LOC102178767, LOC102179881, LOC106503203, LOC108638293, and LOC108638298 genes, were screened. Through qRT-PCR, it was found that there were significant differences in these candidate genes between the two hair types, and most of them had a significant positive correlation with hair length. It was preliminarily inferred that these candidate genes could regulate the different hair types of cashmere goats and provide molecular markers for hair growth.

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Affiliation(s)

Gao Gong College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
Yixing Fan College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China;
Wenze Li College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
Xiaochun Yan College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
Xiaomin Yan College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
Ludan Zhang College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
Na Wang Inner Mongolia Yiwei White Cashmere Goat Co., Ltd., Hohhot 010018, China; (N.W.); (O.C.)
Oljibilig Chen Inner Mongolia Yiwei White Cashmere Goat Co., Ltd., Hohhot 010018, China; (N.W.); (O.C.)
Yanjun Zhang College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
Ruijun Wang College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
Zhihong Liu College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
Wei Jiang College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.)
Jinquan Li College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.) Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot 010018, China Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Agricultural University, Hohhot 010018, China
Zhiying Wang College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.) Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot 010018, China Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Agricultural University, Hohhot 010018, China
Qi Lv College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.) Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot 010018, China Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Agricultural University, Hohhot 010018, China Correspondence: (Q.L.); (R.S.)
Rui Su College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (G.G.); (W.L.); (X.Y.); (X.Y.); (L.Z.); (Y.Z.); (R.W.); (Z.L.); (W.J.); (J.L.); (Z.W.) Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot 010018, China Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Agricultural University, Hohhot 010018, China Correspondence: (Q.L.); (R.S.)

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Wang Z, Hao D, Fang D, Yu J, Wang X, Qin G. Transcriptome Analysis Reveal Candidate Genes and Pathways Responses to Lactate Dehydrogenase Inhibition (Oxamate) in Hyperglycemic Human Renal Proximal Epithelial Tubular Cells. Front Endocrinol (Lausanne) 2022;13:785605. [PMID: 35370938 PMCID: PMC8970056 DOI: 10.3389/fendo.2022.785605] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/21/2022] [Indexed: 11/24/2022] Open

Abstract

Diabetic kidney disease (DKD) is the leading cause of both chronic kidney disease (CKD) and end-stage renal disease (ESRD). Previous studies showed that oxamate could regulate glycemic homeostasis and impacted mitochondria respiration in a hyperglycemia-dependent manner in the rat proximal tubular cells. To explore the transcriptome gene expression profiling of kidney tissues in human renal proximal epithelial tubular cell line (HK-2), we treated HK-2 cells with high D-glucose (HG) for 7 days before the addition of 40 mM oxamate for a further 24 hours in the presence of HG in this study. Afterwards, we identified 3,884 differentially expressed (DE) genes based on adjusted P-value ≤ 0.05 and investigated gene relationships based on weighted gene co-expression network analysis (WGCNA). After qRT-PCR validations, MAP1LC3A, MAP1LC3B (P-value < 0.01) and BECN1 were found to show relatively higher expression levels in the treated groups than the control groups, while PGC1α (P-value < 0.05) showed the lower expressions. Accordingly, enrichment analyses of GO terms and KEGG pathways showed that several pathways [e.g., lysosome pathway (hsa04142) and p53 signaling pathway (hsa04115)] may be involved in the response of HK-2 cells to oxamate. Moreover, via WGCNA, we identified two modules: both the turquoise and blue modules were enriched in pathways associated with lysosome. However, the p53 signaling pathway was only found using all 3,884 DE genes. Furthermore, the key hub genes IGFBP3 (adjusted P-value = 1.34×10^-75 and log₂(FC) = 2.64) interacted with 6 up-regulated and 12 down-regulated DE genes in the network that were enriched in the p53 signaling pathway. This is the first study reporting co-expression patterns of a gene network after lactate dehydrogenase inhibition in HK-2 cells. Our results may contribute to our understanding of the underlying molecular mechanism of in vitro reprogramming under hyperglycemic stress that orchestrates the survival and functions of HK-2 cells.

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