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Co-Expression Network and Integrative Analysis of Metabolome and Transcriptome Uncovers Biological Pathways for Fertility in Beef Heifers

Reproductive failure remains a significant challenge to the beef industry. The omics technologies have provided opportunities to improve reproductive efficiency. We used a multistaged analysis from blood profiles to integrate metabolome (plasma) and transcriptome (peripheral white blood cells) in be...

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Autores principales: Banerjee, Priyanka, Rodning, Soren P., Diniz, Wellison J. S., Dyce, Paul W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9413342/
https://www.ncbi.nlm.nih.gov/pubmed/36005579
http://dx.doi.org/10.3390/metabo12080708
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author Banerjee, Priyanka
Rodning, Soren P.
Diniz, Wellison J. S.
Dyce, Paul W.
author_facet Banerjee, Priyanka
Rodning, Soren P.
Diniz, Wellison J. S.
Dyce, Paul W.
author_sort Banerjee, Priyanka
collection PubMed
description Reproductive failure remains a significant challenge to the beef industry. The omics technologies have provided opportunities to improve reproductive efficiency. We used a multistaged analysis from blood profiles to integrate metabolome (plasma) and transcriptome (peripheral white blood cells) in beef heifers. We used untargeted metabolomics and RNA-Seq paired data from six AI-pregnant (AI-P) and six nonpregnant (NP) Angus-Simmental crossbred heifers at artificial insemination (AI). Based on network co-expression analysis, we identified 17 and 37 hub genes in the AI-P and NP groups, respectively. Further, we identified TGM2, TMEM51, TAC3, NDRG4, and PDGFB as more connected in the NP heifers’ network. The NP gene network showed a connectivity gain due to the rewiring of major regulators. The metabolomic analysis identified 18 and 15 hub metabolites in the AI-P and NP networks. Tryptophan and allantoic acid exhibited a connectivity gain in the NP and AI-P networks, respectively. The gene–metabolite integration identified tocopherol-a as positively correlated with ENSBTAG00000009943 in the AI-P group. Conversely, tocopherol-a was negatively correlated in the NP group with EXOSC2, TRNAUIAP, and SNX12. In the NP group, α-ketoglutarate-SMG8 and putrescine-HSD17B13 were positively correlated, whereas a-ketoglutarate-ALAS2 and tryptophan-MTMR1 were negatively correlated. These multiple interactions identified novel targets and pathways underlying fertility in bovines.
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spelling pubmed-94133422022-08-27 Co-Expression Network and Integrative Analysis of Metabolome and Transcriptome Uncovers Biological Pathways for Fertility in Beef Heifers Banerjee, Priyanka Rodning, Soren P. Diniz, Wellison J. S. Dyce, Paul W. Metabolites Article Reproductive failure remains a significant challenge to the beef industry. The omics technologies have provided opportunities to improve reproductive efficiency. We used a multistaged analysis from blood profiles to integrate metabolome (plasma) and transcriptome (peripheral white blood cells) in beef heifers. We used untargeted metabolomics and RNA-Seq paired data from six AI-pregnant (AI-P) and six nonpregnant (NP) Angus-Simmental crossbred heifers at artificial insemination (AI). Based on network co-expression analysis, we identified 17 and 37 hub genes in the AI-P and NP groups, respectively. Further, we identified TGM2, TMEM51, TAC3, NDRG4, and PDGFB as more connected in the NP heifers’ network. The NP gene network showed a connectivity gain due to the rewiring of major regulators. The metabolomic analysis identified 18 and 15 hub metabolites in the AI-P and NP networks. Tryptophan and allantoic acid exhibited a connectivity gain in the NP and AI-P networks, respectively. The gene–metabolite integration identified tocopherol-a as positively correlated with ENSBTAG00000009943 in the AI-P group. Conversely, tocopherol-a was negatively correlated in the NP group with EXOSC2, TRNAUIAP, and SNX12. In the NP group, α-ketoglutarate-SMG8 and putrescine-HSD17B13 were positively correlated, whereas a-ketoglutarate-ALAS2 and tryptophan-MTMR1 were negatively correlated. These multiple interactions identified novel targets and pathways underlying fertility in bovines. MDPI 2022-07-29 /pmc/articles/PMC9413342/ /pubmed/36005579 http://dx.doi.org/10.3390/metabo12080708 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Banerjee, Priyanka
Rodning, Soren P.
Diniz, Wellison J. S.
Dyce, Paul W.
Co-Expression Network and Integrative Analysis of Metabolome and Transcriptome Uncovers Biological Pathways for Fertility in Beef Heifers
title Co-Expression Network and Integrative Analysis of Metabolome and Transcriptome Uncovers Biological Pathways for Fertility in Beef Heifers
title_full Co-Expression Network and Integrative Analysis of Metabolome and Transcriptome Uncovers Biological Pathways for Fertility in Beef Heifers
title_fullStr Co-Expression Network and Integrative Analysis of Metabolome and Transcriptome Uncovers Biological Pathways for Fertility in Beef Heifers
title_full_unstemmed Co-Expression Network and Integrative Analysis of Metabolome and Transcriptome Uncovers Biological Pathways for Fertility in Beef Heifers
title_short Co-Expression Network and Integrative Analysis of Metabolome and Transcriptome Uncovers Biological Pathways for Fertility in Beef Heifers
title_sort co-expression network and integrative analysis of metabolome and transcriptome uncovers biological pathways for fertility in beef heifers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9413342/
https://www.ncbi.nlm.nih.gov/pubmed/36005579
http://dx.doi.org/10.3390/metabo12080708
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