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Badia-Bringué G, Canive M, Fernandez-Jimenez N, Lavín JL, Casais R, Blanco-Vázquez C, Vázquez P, Fernández A, Bilbao JR, Garrido JM, Juste RA, González-Recio O, Alonso-Hearn M. Summary-data based Mendelian randomization identifies gene expression regulatory polymorphisms associated with bovine paratuberculosis by modulation of the nuclear factor Kappa β ( NF-κß)-mediated inflammatory response. BMC Genomics 2023; 24:605. [PMID: 37821814 PMCID: PMC10568764 DOI: 10.1186/s12864-023-09710-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified host genetic variants associated with paratuberculosis (PTB) susceptibility. Most of the GWAS-identified SNPs are in non-coding regions. Connecting these non-coding variants and downstream affected genes is a challenge and, up to date, only a few functional mutations or expression quantitative loci (cis-eQTLs) associated with PTB susceptibility have been identified. In the current study, the associations between imputed whole-genome sequence genotypes and whole RNA-Sequencing data from peripheral blood (PB) and ileocecal valve (ICV) samples of Spanish Holstein cows (N = 16) were analyzed with TensorQTL. This approach allowed the identification of 88 and 37 cis-eQTLs regulating the expression levels of 90 and 37 genes in PB and ICV samples, respectively (False discorey rate, FDR ≤ 0.05). Next, we applied summary-based data Mendelian randomization (SMR) to integrate the cis-eQTL dataset with GWAS data obtained from a cohort of 813 culled cattle that were classified according to the presence or absence of PTB-associated histopathological lesions in gut tissues. After multiple testing corrections (FDR ≤ 0.05), we identified two novel cis-eQTLs affecting the expression of the early growth response factor 4 (EGR4) and the bovine neuroblastoma breakpoint family member 6-like protein isoform 2 (MGC134040) that showed pleiotropic associations with the presence of multifocal and diffuse lesions in gut tissues; P = 0.002 and P = 0.017, respectively. While EGR4 acts as a brake on T-cell proliferation and cytokine production through interaction with the nuclear factor Kappa β (NF-κß), MGC134040 is a target gene of NF-κß. Our findings provide a better understanding of the genetic factors influencing PTB outcomes, confirm that the multifocal lesions are localized/confined lesions that have different underlying host genetics than the diffuse lesions, and highlight regulatory SNPs and regulated-gene targets to design future functional studies.
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Affiliation(s)
- Gerard Badia-Bringué
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
- Doctoral Program in Molecular Biology and Biomedicine, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Bizkaia, Spain
| | - Maria Canive
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia HRI, Leioa, Bizkaia, Spain
| | - José Luis Lavín
- Department of Applied Mathematics, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Rosa Casais
- Center of Animal Biotechnology, SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Asturias, Spain
| | - Cristina Blanco-Vázquez
- Center of Animal Biotechnology, SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Asturias, Spain
| | - Patricia Vázquez
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Jose Ramón Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia HRI, Leioa, Bizkaia, Spain
| | - Joseba M Garrido
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ramón A Juste
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.
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Dai J, Xiang Y, Fu D, Xu L, Jiang J, Xu J. Ficus carica L. Attenuates Denervated Skeletal Muscle Atrophy via PPARα/NF-κB Pathway. Front Physiol 2020; 11:580223. [PMID: 33343385 PMCID: PMC7744683 DOI: 10.3389/fphys.2020.580223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/13/2020] [Indexed: 12/31/2022] Open
Abstract
Treatment options for denervated skeletal muscle atrophy are limited, in part because the underlying molecular mechanisms are not well understood. Unlike previous transcriptomics studies conducted in rodent models of peripheral nerve injury, in the present study, we performed high-throughput sequencing with denervated atrophic biceps muscle and normal (non-denervated) sternocleidomastoid muscle samples obtained from four brachial plexus injury (BPI) patients. We also investigated whether Ficus carica L. (FCL.) extract can suppress denervated muscle atrophy in a mouse model, along with the mechanism of action. We identified 1471 genes that were differentially expressed between clinical specimens of atrophic and normal muscle, including 771 that were downregulated and 700 that were upregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the differentially expressed genes were mainly enriched in the GO terms “structural constituent of muscle,” “Z disc,” “M band,” and “striated muscle contraction,” as well as “Cell adhesion molecules,” “Glycolysis/Gluconeogenesis,” “Peroxisome proliferator-activated receptor alpha (PPARα) signaling pathway,” and “P53 signaling pathway.” In experiments using mice, the reduction in wet weight and myofiber diameter in denervated muscle was improved by FCL. extract compared to saline administration, which was accompanied by downregulation of the proinflammatory cytokines interleukin (IL)-1β and IL-6. Moreover, although both denervated groups showed increased nuclear factor (NF)-κB activation and PPARα expression, the degree of NF-κB activation was lower while PPARα and inhibitor of NF-κB IκBα expression was higher in FCL. extract-treated mice. Thus, FCL. extract suppresses denervation-induced inflammation and attenuates muscle atrophy by enhancing PPARα expression and inhibiting NF-κB activation. These findings suggest that FCL. extract has therapeutic potential for preventing denervation-induced muscle atrophy caused by peripheral nerve injury or disease.
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Affiliation(s)
- Junxi Dai
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai, China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai, China
| | - Yaoxian Xiang
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai, China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai, China
| | - Da Fu
- Central Laboratory, Shanghai Tenth People's Hospital, Shanghai, China
| | - Lei Xu
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai, China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai, China
| | - Junjian Jiang
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai, China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai, China
| | - Jianguang Xu
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai, China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai, China.,School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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