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Ahmmed R, Hossen MB, Ajadee A, Mahmud S, Ali MA, Mollah MMH, Reza MS, Islam MA, Mollah MNH. Bioinformatics analysis to disclose shared molecular mechanisms between type-2 diabetes and clear-cell renal-cell carcinoma, and therapeutic indications. Sci Rep 2024; 14:19133. [PMID: 39160196 PMCID: PMC11333728 DOI: 10.1038/s41598-024-69302-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/02/2024] [Indexed: 08/21/2024] Open
Abstract
Type 2 diabetes (T2D) and Clear-cell renal cell carcinoma (ccRCC) are both complicated diseases which incidence rates gradually increasing. Population based studies show that severity of ccRCC might be associated with T2D. However, so far, no researcher yet investigated about the molecular mechanisms of their association. This study explored T2D and ccRCC causing shared key genes (sKGs) from multiple transcriptomics profiles to investigate their common pathogenetic processes and associated drug molecules. We identified 259 shared differentially expressed genes (sDEGs) that can separate both T2D and ccRCC patients from control samples. Local correlation analysis based on the expressions of sDEGs indicated significant association between T2D and ccRCC. Then ten sDEGs (CDC42, SCARB1, GOT2, CXCL8, FN1, IL1B, JUN, TLR2, TLR4, and VIM) were selected as the sKGs through the protein-protein interaction (PPI) network analysis. These sKGs were found significantly associated with different CpG sites of DNA methylation that might be the cause of ccRCC. The sKGs-set enrichment analysis with Gene Ontology (GO) terms and KEGG pathways revealed some crucial shared molecular functions, biological process, cellular components and KEGG pathways that might be associated with development of both T2D and ccRCC. The regulatory network analysis of sKGs identified six post-transcriptional regulators (hsa-mir-93-5p, hsa-mir-203a-3p, hsa-mir-204-5p, hsa-mir-335-5p, hsa-mir-26b-5p, and hsa-mir-1-3p) and five transcriptional regulators (YY1, FOXL1, FOXC1, NR2F1 and GATA2) of sKGs. Finally, sKGs-guided top-ranked three repurposable drug molecules (Digoxin, Imatinib, and Dovitinib) were recommended as the common treatment for both T2D and ccRCC by molecular docking and ADME/T analysis. Therefore, the results of this study may be useful for diagnosis and therapies of ccRCC patients who are also suffering from T2D.
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Affiliation(s)
- Reaz Ahmmed
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
- Department of Biochemistry & Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Bayazid Hossen
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
- Department of Agricultural and Applied Statistics, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Alvira Ajadee
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Sabkat Mahmud
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Ahad Ali
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
- Department of Chemistry, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Manir Hossain Mollah
- Department of Physical Sciences, Independent University, Bangladesh (IUB), Dhaka, Bangladesh
| | - Md Selim Reza
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
- Division of Biomedical Informatics and Genomics, School of Medicine, Tulane University, 1440 Canal St., RM 1621C, New Orleans, LA, 70112, USA
| | - Mohammad Amirul Islam
- Department of Biochemistry & Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Nurul Haque Mollah
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
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Kober AKMH, Saha S, Ayyash M, Namai F, Nishiyama K, Yoda K, Villena J, Kitazawa H. Insights into the Anti-Adipogenic and Anti-Inflammatory Potentialities of Probiotics against Obesity. Nutrients 2024; 16:1373. [PMID: 38732619 PMCID: PMC11085650 DOI: 10.3390/nu16091373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Functional foods with probiotics are safe and effective dietary supplements to improve overweight and obesity. Thus, altering the intestinal microflora may be an effective approach for controlling or preventing obesity. This review aims to summarize the experimental method used to study probiotics and obesity, and recent advances in probiotics against obesity. In particular, we focused on studies (in vitro and in vivo) that used probiotics to treat obesity and its associated comorbidities. Several in vitro and in vivo (animal and human clinical) studies conducted with different bacterial species/strains have reported that probiotics promote anti-obesity effects by suppressing the differentiation of pre-adipocytes through immune cell activation, maintaining the Th1/Th2 cytokine balance, altering the intestinal microbiota composition, reducing the lipid profile, and regulating energy metabolism. Most studies on probiotics and obesity have shown that probiotics are responsible for a notable reduction in weight gain and body mass index. It also increases the levels of anti-inflammatory adipokines and decreases those of pro-inflammatory adipokines in the blood, which are responsible for the regulation of glucose and fatty acid breakdown. Furthermore, probiotics effectively increase insulin sensitivity and decrease systemic inflammation. Taken together, the intestinal microbiota profile found in overweight individuals can be modified by probiotic supplementation which can create a promising environment for weight loss along enhancing levels of adiponectin and decreasing leptin, tumor necrosis factor (TNF)-α, interleukin (IL)-6, monocyte chemotactic protein (MCP)-1, and transforming growth factor (TGF)-β on human health.
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Affiliation(s)
- A. K. M. Humayun Kober
- Department of Dairy and Poultry Science, Chittagong Veterinary and Animal Sciences University, Khulshi, Chittagong 4225, Bangladesh;
| | - Sudeb Saha
- Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8576, Japan; (F.N.); (K.N.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Tohoku University, Sendai 980-8576, Japan
- Department of Dairy Science, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mutamed Ayyash
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates;
| | - Fu Namai
- Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8576, Japan; (F.N.); (K.N.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Tohoku University, Sendai 980-8576, Japan
| | - Keita Nishiyama
- Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8576, Japan; (F.N.); (K.N.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Tohoku University, Sendai 980-8576, Japan
| | - Kazutoyo Yoda
- Technical Research Laboratory, Takanashi Milk Products Co., Ltd., Yokohama 241-0023, Japan;
| | - Julio Villena
- Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8576, Japan; (F.N.); (K.N.)
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucuman 4000, Argentina
| | - Haruki Kitazawa
- Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8576, Japan; (F.N.); (K.N.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Tohoku University, Sendai 980-8576, Japan
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3
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Su YY, Liu YL, Huang HC, Lin CC. Ensemble learning model for identifying the hallmark genes of NFκB/TNF signaling pathway in cancers. J Transl Med 2023; 21:485. [PMID: 37475016 PMCID: PMC10357720 DOI: 10.1186/s12967-023-04355-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND The nuclear factor kappa B (NFκB) regulatory pathways downstream of tumor necrosis factor (TNF) play a critical role in carcinogenesis. However, the widespread influence of NFκB in cells can result in off-target effects, making it a challenging therapeutic target. Ensemble learning is a machine learning technique where multiple models are combined to improve the performance and robustness of the prediction. Accordingly, an ensemble learning model could uncover more precise targets within the NFκB/TNF signaling pathway for cancer therapy. METHODS In this study, we trained an ensemble learning model on the transcriptome profiles from 16 cancer types in the TCGA database to identify a robust set of genes that are consistently associated with the NFκB/TNF pathway in cancer. Our model uses cancer patients as features to predict the genes involved in the NFκB/TNF signaling pathway and can be adapted to predict the genes for different cancer types by switching the cancer type of patients. We also performed functional analysis, survival analysis, and a case study of triple-negative breast cancer to demonstrate our model's potential in translational cancer medicine. RESULTS Our model accurately identified genes regulated by NFκB in response to TNF in cancer patients. The downstream analysis showed that the identified genes are typically involved in the canonical NFκB-regulated pathways, particularly in adaptive immunity, anti-apoptosis, and cellular response to cytokine stimuli. These genes were found to have oncogenic properties and detrimental effects on patient survival. Our model also could distinguish patients with a specific cancer subtype, triple-negative breast cancer (TNBC), which is known to be influenced by NFκB-regulated pathways downstream of TNF. Furthermore, a functional module known as mononuclear cell differentiation was identified that accurately predicts TNBC patients and poor short-term survival in non-TNBC patients, providing a potential avenue for developing precision medicine for cancer subtypes. CONCLUSIONS In conclusion, our approach enables the discovery of genes in NFκB-regulated pathways in response to TNF and their relevance to carcinogenesis. We successfully categorized these genes into functional groups, providing valuable insights for discovering more precise and targeted cancer therapeutics.
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Affiliation(s)
- Yin-Yuan Su
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Ling Liu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Division of General Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chen-Ching Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Liu L, Zhang Y, Ma H, Cao H, Liu W. Integrating genome-wide methylation and transcriptome-wide analyses to reveal the genetic mechanism of milk traits in Kazakh horses. Gene 2023; 856:147143. [PMID: 36574934 DOI: 10.1016/j.gene.2022.147143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Horse Milk has important quantitative characteristics and high economic value. However, the DNA methylation regulators involved in horse milk traits have not been clarified. To explore the important role of genome-wide DNA methylation in regulating equine milk yield, this study systematically investigated the genome-wide DNA methylation profiles of Kazakh horse blood by comparing a high-production group (HP, average daily milk yield of 7.5 kg) and low-production group (LP, average daily milk yield of 3.2 kg) using deep whole-genome bisulfite sequencing. First, both groups showed similar proportions of methylation at CpG sites. Subsequently, we identified 26,677 differential methylated regions (DMRs) of CG, 15 DMRs of CHG, 480 DMRs of CHH and 8268 DMR-related genes (DMGs). GO and KEGG analyses revealed that some DMGs were involved in regulating milk and milk component formation. By combining the WGBS-seq and the previous RNA-seq data, a total of 94 overlapping genes were obtained. Finally, we found that 9 DMGs are likely involved in milk production by Kazakh horses.
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Affiliation(s)
- Lingling Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yunting Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Haiyu Ma
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hang Cao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
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Zhao L, Wang W, Wang X, Zhang D, Li X, Zhao Y, Zhang Y, Xu D, Cheng J, Wang J, Li W, Lin C, Wu W, Zhang X, Zheng W. Identification of SNPs and expression patterns of ALB, AHSG and GC genes and their association with growth traits in Hu sheep. Gene 2023; 853:147100. [PMID: 36470483 DOI: 10.1016/j.gene.2022.147100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Growth traits are economically important traits in sheep breeding. This study was conducted to evaluate the polymorphisms of ALB, AHSG and GC genes and their association with growth traits in Hu sheep. We measured and recorded the body weight (BW), body height (BH), body length (BL) and feed conversion ratio (FCR) of 1418 male Hu sheep raised in the same environment from 80 to 180 days of age. The total of four SNPs in the ALB, AHSG and GC genes were identified by direct sequencing technology. The results of association analysis showed that two loci (g.8699 A>T and g.13458 T>C) of ALB gene significantly affect average daily gain (ADG; P < 0.05). The genotypes of SNP g.2454 T>C in AHSG gene were significantly associated with ADG and FCR (P < 0.05). There were significant associations between GC g.19484 A>C and BW, BH and BL (P < 0.05). The results of qRT-PCR showed that ALB, AHSG, and GC genes were extremely significantly higher in H_BW sheep compared with those in the L_BW sheep (P < 0.01). These results revealed that ALB-1 g.8699 A>T, ALB-2 g.13458 T>C, AHSG g.2454 T>C and GC g.19484 A>C loci are potential molecular markers for Hu sheep breeding.
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Affiliation(s)
- Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China; The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang 830000, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang 830000, China.
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6
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Li A, Li Y, Wang Y, Wang Y, Li X, Qubi W, Xiong Y, Zhu J, Liu W, Lin Y. ACADL Promotes the Differentiation of Goat Intramuscular Adipocytes. Animals (Basel) 2023; 13:ani13020281. [PMID: 36670821 PMCID: PMC9854987 DOI: 10.3390/ani13020281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
Intramuscular fat (IMF) deposits help improve meat quality such as marbling, juicy, flavor and tenderness. Long-chain acyl-CoA dehydrogenase (ACADL) is a key enzyme for catalyzing fatty acid oxidation, and studies have shown ACADL is involved in the deposition and differentiation of intramuscular adipocytes. However, the effect of ACADL on intramuscular adipocytes differentiation in goats needs further study. In this study, to explore the mechanism of ACADL on the development of goat intramuscular adipocytes, we constructed an over-expression plasmids and a SI-RNA of ACADL to explore the function of ACADL on the development of goat IMF. It was found that overexpression of ACADL promoted the differentiation of goat intramuscular adipocytes, and promoted the expression of fat cell differentiation marker genes lipoprotein lipase (LPL), peroxisome proliferator activated receptor gamma (PPARγ), APETALA-2-like transcription factor gene (AP2), CCAT enhancer binding protein (CEBPα), preadipocyte Factor 1 (Pref-1) and CCAT enhancer binding protein (CEBPβ), and the opposite trend occurred after interference. In addition, we screened of this related tumor necrosis factor (TNF) signaling pathway by RNA-Seq. So, we validate the signaling pathway with inhibitor of TNF signaling pathway. In summary, these results indicate that ACADL promotes intramuscular adipocytes differentiation through activation TNF signaling pathway. This study provides an important basis for the mechanism of IMF development.
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Affiliation(s)
- An Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Southwest Minzu University, Chengdu 610041, China
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China
| | - Yanyan Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Southwest Minzu University, Chengdu 610041, China
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China
| | - Youli Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Southwest Minzu University, Chengdu 610041, China
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China
| | - Yong Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Southwest Minzu University, Chengdu 610041, China
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China
| | - Xin Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Southwest Minzu University, Chengdu 610041, China
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China
| | - Wuqie Qubi
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Southwest Minzu University, Chengdu 610041, China
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China
| | - Yan Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Southwest Minzu University, Chengdu 610041, China
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China
| | - Jiangjiang Zhu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Southwest Minzu University, Chengdu 610041, China
| | - Wei Liu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Southwest Minzu University, Chengdu 610041, China
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China
| | - Yaqiu Lin
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Southwest Minzu University, Chengdu 610041, China
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China
- Correspondence: ; Tel./Fax: +86-028-85522310
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7
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Zhao L, Li F, Zhang X, Zhang D, Li X, Zhang Y, Zhao Y, Song Q, Huang K, Xu D, Cheng J, Wang J, Li W, Lin C, Wang W. Integrative analysis of transcriptomics and proteomics of longissimus thoracis of the Hu sheep compared with the Dorper sheep. Meat Sci 2022; 193:108930. [PMID: 35933909 DOI: 10.1016/j.meatsci.2022.108930] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/09/2022] [Accepted: 07/29/2022] [Indexed: 10/31/2022]
Abstract
Meat quality is becoming more important for sheep breeding programs. Meat quality is a complex trait affected by genetic and environmental factors. In the present study, an integrative analysis of the longissimus thoracis tissue transcriptome and proteome was conducted to identify genes, proteins, and pathways related to meat quality in sheep. The sheep breeds Hu and Dorper were considered. These breeds were compared for the differences in muscle fiber structure, chemical composition, and amino acid composition. In the Hu sheep vs. Dorper sheep comparison, 22 DEGs/DEPs showed the same mRNA and protein expression trends. These genes are associated with lipid transport, lipid metabolism, and muscular system development. Moreover, some pathways such as "lipid transport", "lipoprotein metabolic process", "Alanine, aspartate and glutamate metabolism", and "Arginine biosynthesis" were significantly enriched in this study. The reliability of the RNA-Seq results was verified by qRT-PCR. These findings provide new insights into the molecular mechanisms of meat quality in sheep.
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Affiliation(s)
- Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Qizhi Song
- Linze County Animal Disease Prevention and Control Center of Gansu Province, Linze 734200, China
| | - Kai Huang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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8
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Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs. Animals (Basel) 2022; 12:ani12111382. [PMID: 35681846 PMCID: PMC9179479 DOI: 10.3390/ani12111382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Copy number variation (CNV) is a type of variant that may influence meat quality of, for example intramuscular fat (IMF). In this study, a genome-wide association study (GWAS) was then performed between CNVs and IMF in a pig F2 resource population. A total of 19 CNVRs were found to be significantly associated with IMF. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings. Abstract Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality. In this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. In conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings.
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Yan S, Sui M, Tian H, Fu J, Li Y, Chen J, Zeng L, Ding X. Transcriptomic Analysis Revealed an Important Role of Peroxisome-Proliferator-Activated Receptor Alpha Signaling in Src Homology Region 2 Domain-Containing Phosphatase-1 Insufficiency Leading to the Development of Renal Ischemia-Reperfusion Injury. Front Med (Lausanne) 2022; 9:847512. [PMID: 35646989 PMCID: PMC9134314 DOI: 10.3389/fmed.2022.847512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/06/2022] [Indexed: 12/02/2022] Open
Abstract
In kidney transplantation, the donor kidney inevitably undergoes ischemia-reperfusion injury (IRI). It is of great importance to study the pathogenesis of IRI and find effective measures to attenuate acute injury of renal tubules after ischemia-reperfusion. Our previous study found that Src homology region 2 domain-containing phosphatase-1 (SHP-1) insufficiency aggravates renal IRI. In this study, we systematically analyzed differences in the expression profiles of SHP-1 (encoded by Ptpn6)-insufficient mice and wild-type mice by RNA-seq. We found that a total of 161 genes showed at least a twofold change, with a false discovery rate <0.05 in Ptpn6 +/mev mice after IRI and 42 genes showing more than a fourfold change. Of the eight genes encoding proteins with immunoreceptor tyrosine-based inhibitory motifs (ITIMs) that bind to Ptpn6, three were upregulated, and five were downregulated. We found that for the differentially expressed genes (DEGs) with a fold change >2, the most significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were the cell division pathway and peroxisome-proliferator activated receptor PPARα signaling pathways. Furthermore, the downregulated genes of the PPARα signaling pathway were mainly related to fatty acid absorption and degradation. Using an agonist of the PPARα signaling pathway, fenofibrate, we found that renal IRI was significantly attenuated in Ptpn6 +/mev mice. In summary, our results show that insufficiency of SHP-1 inhibits the expression of genes in the PPARα signaling pathway, thereby leading to increased reactive oxygen species (ROS) and exacerbating the renal IRI. The PPARα signaling agonist fenofibrate partially attenuates renal IRI induced by SHP-1 insufficiency.
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Affiliation(s)
- Sijia Yan
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Mingxing Sui
- Department of Organ Transplantation, Changhai Hospital, Navy Medical University, Shanghai, China
| | - Hongzhe Tian
- Department of Urology Surgery-General Hospital of Central Theater Command of PLA, Wuhan, China
| | - Jiazhao Fu
- Department of Organ Transplantation, Changhai Hospital, Navy Medical University, Shanghai, China
| | - Yanfeng Li
- Department of Organ Transplantation, Changhai Hospital, Navy Medical University, Shanghai, China
| | - Jing Chen
- Department of Laboratory and Diagnosis, Changhai Hospital, Navy Medical University, Shanghai, China
| | - Li Zeng
- Department of Organ Transplantation, Changhai Hospital, Navy Medical University, Shanghai, China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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Zhong X, Gu J, Zhang S, Chen X, Zhang J, Miao J, Ding Z, Xu J, Cheng H. Dynamic transcriptome analysis of the muscles in high-fat diet-induced obese zebrafish (Danio rerio) under 5-HT treatment. Gene 2022; 819:146265. [PMID: 35121026 DOI: 10.1016/j.gene.2022.146265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 11/04/2022]
Abstract
Peripheral 5-hydroxytryptamine (5-HT, also called serotonin) is reportedly a potential therapeutic target in obesity-related metabolic diseases due to its regulatory role in energy homeostasis in mammals. However, information on the detailed effect of peripheral 5-HT on the energy metabolism in fishes, especially the lipid metabolism, and the underlying mechanism remains elusive. In this study, a diet-induced obesity model was developed in the zebrafish (Danio rerio), a prototypical animal model for metabolic disorders. The zebrafish were fed a high-fat diet for 8 weeks and were simultaneously injected with PBS, 0.1 mM and 10 mM 5-HT, intraperitoneally. The body weight was significantly lower in the zebrafish injected with 0.1 mM 5-HT (P < 0.05), however, there was no change in body length (P > 0.05) at the end of the 8-week treatment. The muscle tissues from the zebrafish treated with PBS and 5-HT were collected for transcriptomic analysis and the RNA-seq revealed 1134, 3713, and 2535 genes were screened out compared to the muscular DEGs among three groups. The enrichment analysis revealed DEGs to be significantly associated with multiple metabolic pathways, including ribosome, oxidative phosphorylation, proteasome, PPAR signaling pathway, and ferroptosis. Additionally, the qRT-PCR validated 12 DEGs out of which 10 genes exhibited consistent trends. Taken together, this data provided useful information on the transcriptional characteristics of the muscle tissue in the obese zebrafish exposed to 5-HT, offering important insights into the regulatory effect of peripheral 5-HT in teleosts, as well as novel approaches for preventing and treating obesity-related metabolic dysfunction.
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Affiliation(s)
- Xiangqi Zhong
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Key Laboratory of Cultivation and High-value Utilization of Marine Organisms, Fisheries Research Institute of Fujian, Xiamen 361000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jiaze Gu
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Siying Zhang
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiangning Chen
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Key Laboratory of Cultivation and High-value Utilization of Marine Organisms, Fisheries Research Institute of Fujian, Xiamen 361000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
| | - Jingjing Zhang
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jintao Miao
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhujin Ding
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jianhe Xu
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Hanliang Cheng
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
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Zhang C, Wang T, Cui T, Liu S, Zhang B, Li X, Tang J, Wang P, Guo Y, Wang Z. Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family. Evol Bioinform Online 2021; 17:11769343211041382. [PMID: 34471342 PMCID: PMC8404664 DOI: 10.1177/11769343211041382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/02/2021] [Indexed: 11/16/2022] Open
Abstract
The CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into 6 subgroups named C/EBPα, C/EBPβ, C/EBPδ, C/EBPε, C/EBPγ, and C/EBPζ. Gene expression analysis showed that the C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ, and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various pig tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs and miRNAs. A total of 27 feed-forward loop (FFL) motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to FFL sub-network were analyzed in 27 adult pig tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.
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Affiliation(s)
- Chaoxin Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Tao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Tongyan Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Shengwei Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Bing Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Xue Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Jian Tang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Peng Wang
- HeiLongJiang provincial Husbandry Dapartment, Harbin, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- Bioinformatics Center, Northeast Agricultural University, Harbin, China
- DaBeiNong Group, Beijing, China
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Zhou J, Zhang Y, Wu J, Qiao M, Xu Z, Peng X, Mei S. Proteomic and lipidomic analyses reveal saturated fatty acids, phosphatidylinositol, phosphatidylserine, and associated proteins contributing to intramuscular fat deposition. J Proteomics 2021; 241:104235. [PMID: 33894376 DOI: 10.1016/j.jprot.2021.104235] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 12/15/2022]
Abstract
Intramuscular fat (IMF) content is an important factor in porcine meat quality. Previous studies have screened multiple candidate genes related to IMF deposition, but the lipids that affect IMF deposition and their lipid-protein network remain unknown. In this study, we performed proteomic and lipidomic analyses of the longissimus dorsi (LD) muscle from high-IMF (IMFH) and low-IMF (IMF-L) groups of Xidu black pigs. Eighty-eight proteins and 143 lipids were differentially abundant between the groups. The differentially abundant proteins were found to be involved in cholesterol metabolism, the PPAR signaling pathway, and ferroptosis. The triacylglycerols (TAGs) upregulated in the IMF-H group were mainly shown to be synthesized by saturated fatty acids (SFAs), while the downregulated TAGs were mainly synthesized by polyunsaturated fatty acids (PUFAs). All differentially abundant phosphatidylinositols (PIs) and phosphatidylserines (PSs) were found to be upregulated in the IMF-H group. A correlation analysis of the proteomic and lipidomic revealed candidate proteins (APOA4, VDAC3, PRNP, CTSB, GSPT1) related to TAG, PI, and PS lipids. These results revealed differences in proteins and lipids between the IMF-H and IMF-L groups, which represent new candidate proteins and lipids that should be investigated to determine the molecular mechanisms controlling IMF deposition in pigs. SIGNIFICANCE: Intramuscular fat (IMF) is a key factor affecting meat quality, and meat with a higher IMF content can have a better flavor. In this study, proteomic results show that the ferroptosis pathway, including the PRNP, VDAC3 and CP proteins, affects IMF deposition. Lipid composition is the key factor affecting IMF deposition, but there are few reports on this. In this study, through lipidomic analysis, we suggest that saturated fatty acid (SFA), phosphatidylinositol (PI), and phosphatidylserine (PS) may contribute to IMF deposition. A correlation analysis reveals the potential regulatory network between lipids and proteins. This study clarifies the difference in protein and lipid compositions in longissimus dorsi (LD) muscle with high and low IMF contents. This information suggests that it would be beneficial to increase the intramuscular fat content of pork not only from a genetic perspective but also from a nutritional perspective.
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Affiliation(s)
- Jiawei Zhou
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Yu Zhang
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Junjing Wu
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Mu Qiao
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Zhong Xu
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Xianwen Peng
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Shuqi Mei
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China.
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Blay C, Haffray P, Bugeon J, D’Ambrosio J, Dechamp N, Collewet G, Enez F, Petit V, Cousin X, Corraze G, Phocas F, Dupont-Nivet M. Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss. Front Genet 2021; 12:639223. [PMID: 33692832 PMCID: PMC7937956 DOI: 10.3389/fgene.2021.639223] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
One of the top priorities of the aquaculture industry is the genetic improvement of economically important traits in fish, such as those related to processing and quality. However, the accuracy of genetic evaluations has been hindered by a lack of data on such traits from a sufficiently large population of animals. The objectives of this study were thus threefold: (i) to estimate genetic parameters of growth-, yield-, and quality-related traits in rainbow trout (Oncorhynchus mykiss) using three different phenotyping technologies [invasive and non-invasive: microwave-based, digital image analysis, and magnetic resonance imaging (MRI)], (ii) to detect quantitative trait loci (QTLs) associated with these traits, and (iii) to identify candidate genes present within these QTL regions. Our study collected data from 1,379 fish on growth, yield-related traits (body weight, condition coefficient, head yield, carcass yield, headless gutted carcass yield), and quality-related traits (total fat, percentage of fat in subcutaneous adipose tissue, percentage of fat in flesh, flesh colour); genotypic data were then obtained for all fish using the 57K SNP Axiom® Trout Genotyping array. Heritability estimates for most of the 14 traits examined were moderate to strong, varying from 0.12 to 0.67. Most traits were clearly polygenic, but our genome-wide association studies (GWASs) identified two genomic regions on chromosome 8 that explained up to 10% of the genetic variance (cumulative effects of two QTLs) for several traits (weight, condition coefficient, subcutaneous and total fat content, carcass and headless gutted carcass yields). For flesh colour traits, six QTLs explained 1-4% of the genetic variance. Within these regions, we identified several genes (htr1, gnpat, ephx1, bcmo1, and cyp2x) that have been implicated in adipogenesis or carotenoid metabolism, and thus represent good candidates for further functional validation. Finally, of the three techniques used for phenotyping, MRI demonstrated particular promise for measurements of fat content and distribution, while the digital image analysis-based approach was very useful in quantifying colour-related traits. This work provides new insights that may aid the development of commercial breeding programmes in rainbow trout, specifically with regard to the genetic improvement of yield and flesh-quality traits as well as the use of invasive and/or non-invasive technologies to predict such traits.
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Affiliation(s)
- Carole Blay
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | | | - Jonathan D’Ambrosio
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
- SYSAAF, Station LPGP-INRAE, Rennes, France
| | - Nicolas Dechamp
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | | | | | - Xavier Cousin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
| | - Geneviève Corraze
- INRAE, University of Pau & Pays Adour, E2S UPPA, UMR 1419 NuMéA, Saint-Pée-sur-Nivelle, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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Evaluation of Fat Accumulation and Adipokine Production during the Long-Term Adipogenic Differentiation of Porcine Intramuscular Preadipocytes and Study of the Influence of Immunobiotics. Cells 2020; 9:cells9071715. [PMID: 32708964 PMCID: PMC7408200 DOI: 10.3390/cells9071715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/17/2022] Open
Abstract
The degree of fat accumulation and adipokine production are two major indicators of obesity that are correlated with increased adipose tissue mass and chronic inflammatory responses. Adipocytes have been considered effector cells for the inflammatory responses due to their capacity to express Toll-like receptors (TLRs). In this study, we evaluated the degree of fat accumulation and adipokine production in porcine intramuscular preadipocyte (PIP) cells maintained for in vitro differentiation over a long period without or with stimulation of either TNF-α or TLR2-, TLR3-, or TLR4-ligands. The cytosolic fat accumulation was measured by liquid chromatography and the expression of adipokines (CCL2, IL-6, IL-8 and IL-10) were quantified by RT-qPCR and ELISA at several time points (0 to 20 days) of PIP cells differentiation. Long-term adipogenic differentiation (LTAD) induced a progressive fat accumulation in the adipocytes over time. Activation of TLR3 and TLR4 resulted in an increased rate of fat accumulation into the adipocytes over the LTAD. The production of CCL2, IL-8 and IL-6 were significantly increased in unstimulated adipocytes during the LTAD, while IL-10 expression remained stable over the studied period. An increasing trend of adiponectin and leptin production was also observed during the LTAD. On the other hand, the stimulation of adipocytes with TLRs agonists or TNF-α resulted in an increasing trend of CCL2, IL-6 and IL-8 production while IL-10 remained stable in all four treatments during the LTAD. We also examined the influences of several immunoregulatory probiotic strains (immunobiotics) on the modulation of the fat accumulation and adipokine production using supernatants of immunobiotic-treated intestinal immune cells and the LTAD of PIP cells. Immunobiotics have shown a strain-specific ability to modulate the fat accumulation and adipokine production, and differentiation of adipocytes. Here, we expanded the utility and potential application of our in vitro PIP cells model by evaluating an LTAD period (20 days) in order to elucidate further insights of chronic inflammatory pathobiology of adipocytes associated with obesity as well as to explore the prospects of immunomodulatory intervention for obesity such as immunobiotics.
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De Deurwaerdère P, Di Giovanni G. Serotonin in Health and Disease. Int J Mol Sci 2020; 21:ijms21103500. [PMID: 32429111 PMCID: PMC7278959 DOI: 10.3390/ijms21103500] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023] Open
Abstract
The International Journal of Molecular Sciences Special Issue "Serotonin in health and diseases" covers several aspects of the multiple and still mysterious functions of serotonin (5-hydroxytryptamine; 5-HT). 5-HT is neurotransmitter acting in the central nervous system (CNS), blood factor, and neurohormone controlling the function of several peripheral organs. Beyond its widespread implication in physiology, the 5-HT system is involved in numerous diseases of the CNS (e.g., depression, anxiety, schizophrenia, obsessive-compulsive disorders, addiction, Parkinson's disease) and peripheral organs (e.g., gastrointestinal disorders, cardiac arrhythmia, hypertension). The Special Issue includes 14 articles dealing with molecular and cellular effects of 5-HT in periphery and CNS, from functional aspects in lower animals to clinical practices. Beyond physiology, the Special Issue also covers the influence of 5-HT and its receptors in the mechanism of action of psychoactive molecules including antipsychotics, antidepressants, and drug of abuse. The recent progress made on the function and dysfunction of the 5-HT system will certainly increase the understanding of the widespread role of 5-HT ultimately leading to better apprehend its targeting in human diseases.
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Affiliation(s)
- Philippe De Deurwaerdère
- Centre National de la Recherche Scientifique, UMR CNRS 5287, CEDEX F-33000 Bordeaux, France
- Correspondence: (P.D.D.); (G.D.G.)
| | - Giuseppe Di Giovanni
- Laboratory of Neurophysiology, Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD2080 Msida, Malta
- School of Biosciences, Neuroscience Division, Cardiff University, Cardiff CF10 3AX, UK
- Correspondence: (P.D.D.); (G.D.G.)
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