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Yu J, Li X, Qi X, Ding Z, Su S, Yu L, Zhou L, Li Y. Translatomics reveals the role of dietary calcium addition in regulating muscle fat deposition in pigs. Sci Rep 2024; 14:12295. [PMID: 38811812 PMCID: PMC11136974 DOI: 10.1038/s41598-024-62986-0] [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: 02/15/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024] Open
Abstract
Intramuscular fat (IMF) in pork holds significant importance for economic performance within the pig industry and dietary calcium supplementation enhances the accumulation of intramuscular fat. Additionally, calcium ions inhibit translation and reduce protein synthesis. However, the mechanism by which calcium regulates IMF deposition in muscle through translation remains largely unknown. In this study, we compared the ribosome profiles of the longissimus dorsi muscles of Duroc × Landrace × Large white pigs from the normal calcium (NC) group or calcium supplement (HC) group by Ribo-seq, and RNA-seq. By integrating multiple-omics analysis, we further discovered 437 genes that were transcriptionally unchanged but translationally altered and these genes were significantly enriched in the oxidative phosphorylation signaling pathway. Furthermore, experimental data showed that inhibiting the expression of COX10 and mtND4L increased triglyceride accumulation in C2C12 cells, providing new targets for intramuscular fat deposition. Finally, this work links dietary calcium, translation regulation and IMF deposition, providing a new strategy for both meat quality and economic performance within the pig industry.
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Affiliation(s)
- Jingsu Yu
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Xiangling Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Xinyu Qi
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Zhaoxuan Ding
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Songtao Su
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Lin Yu
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Lei Zhou
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China.
| | - Yixing Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China.
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2
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Xu G, Pan H, Fan L, Zhang L, Li J, Cheng S, Meng L, Shen N, Liu Y, Li Y, Huang T, Zhou L. Dietary Betaine Improves Glucose Metabolism in Obese Mice. J Nutr 2024; 154:1309-1320. [PMID: 38417550 DOI: 10.1016/j.tjnut.2024.02.025] [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: 11/26/2023] [Revised: 02/17/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Obesity caused by the overconsumption of energy-dense foods high in fat and sugar has contributed to the growing prevalence of type 2 diabetes. Betaine, found in food or supplements, has been found to lower blood glucose concentrations, but its exact mechanism of action is not well understood. OBJECTIVES A comprehensive evaluation of the potential mechanisms by which betaine supplementation improves glucose metabolism. METHODS Hyperglycemic mice were fed betaine to measure the indexes of glucose metabolism in the liver and muscle. To explore the mechanism behind the regulation of betaine on glucose metabolism, Ribonucleic Acid-Seq was used to analyze the livers of the mice. In vitro, HepG2 and C2C12 cells were treated with betaine to more comprehensively evaluate the effect of betaine on glucose metabolism. RESULTS Betaine was added to the drinking water of high-fat diet-induced mice, and it was found to reduce blood glucose concentrations and liver triglyceride concentrations without affecting body weight, confirming its hypoglycemic effect. To investigate the specific mechanism underlying its hypoglycemic effect, protein-protein interaction enrichment analysis of the liver revealed key nodes associated with glucose metabolism, including cytochrome P450 family activity, insulin sensitivity, glucose homeostasis, and triglyceride concentrations. The Kyoto Encyclopedia of Genes and Genomes and gene ontogeny enrichment analyses showed significant enrichment of the Notch signaling pathway. These results provided bioinformatic evidence for specific pathways through which betaine regulates glucose metabolism. Key enzyme activities involved in glucose uptake, glycogen synthesis, and glycogenolysis pathways of the liver and muscle were measured, and improvements were observed in these pathways. CONCLUSIONS This study provides new insight into the mechanisms by which betaine improves glucose metabolism in the liver and muscle and supports its potential as a drug for the treatment of metabolic disorders related to glucose.
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Affiliation(s)
- Gaoxiao Xu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Hongyuan Pan
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Liping Fan
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Lifang Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Jian Li
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Shimei Cheng
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Libing Meng
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Nana Shen
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Yong Liu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Yixing Li
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Tengda Huang
- College of Animal Science and Technology, Guangxi University, Nanning, China.
| | - Lei Zhou
- Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
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Tang X, Li Q, Feng X, Yang B, Zhong X, Zhou Y, Wang Q, Mao Y, Xie W, Liu T, Tang Q, Guo W, Wu F, Feng X, Wang Q, Lu Y, Xu J. Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots. Int J Mol Sci 2023; 24:15039. [PMID: 37894720 PMCID: PMC10606207 DOI: 10.3390/ijms242015039] [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: 07/25/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts with lengths of more than 200 nt and limited protein-coding potential. They were found to play important roles in plant stress responses. In this study, the maize drought-tolerant inbred line AC7643 and drought-sensitive inbred line AC7729/TZSRW, as well as their recombinant inbred lines (RILs) were selected to identify drought-responsive lncRNAs in roots. Compared with non-responsive lncRNAs, drought-responsive lncRNAs had different sequence characteristics in length of genes and number of exons. The ratio of down-regulated lncRNAs induced by drought was significantly higher than that of coding genes; and lncRNAs were more widespread expressed in recombination sites in the RILs. Additionally, by integration of the modifications of DNA 5-methylcytidine (5mC), histones, and RNA N6-methyladenosine (m6A), it was found that the enrichment of histone modifications associated with transcriptional activation in the genes generated lncRNAs was lower that coding genes. The lncRNAs-mRNAs co-expression network, containing 15,340 coding genes and 953 lncRNAs, was constructed to investigate the molecular functions of lncRNAs. There are 13 modules found to be associated with survival rate under drought. We found nine SNPs located in lncRNAs among the modules associated with plant survival under drought. In conclusion, we revealed the characteristics of lncRNAs responding to drought in maize roots based on multiomics studies. These findings enrich our understanding of lncRNAs under drought and shed light on the complex regulatory networks that are orchestrated by the noncoding RNAs in response to drought stress.
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Affiliation(s)
- Xin Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qimeng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoju Feng
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiu Zhong
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Mao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Wubin Xie
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianhong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Guo
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuanjun Feng
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qingjun Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
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Zhang Z, Liao Q, Pan T, Yu L, Luo Z, Su S, Liu S, Hou M, Li Y, Damba T, Liang Y, Zhou L. BATF relieves hepatic steatosis by inhibiting PD1 and promoting energy metabolism. eLife 2023; 12:RP88521. [PMID: 37712938 PMCID: PMC10503959 DOI: 10.7554/elife.88521] [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] [Indexed: 09/16/2023] Open
Abstract
The rising prevalence of nonalcoholic fatty liver disease (NAFLD) has become a global health threat that needs to be addressed urgently. Basic leucine zipper ATF-like transcription factor (BATF) is commonly thought to be involved in immunity, but its effect on lipid metabolism is not clear. Here, we investigated the function of BATF in hepatic lipid metabolism. BATF alleviated high-fat diet (HFD)-induced hepatic steatosis and inhibited elevated programmed cell death protein (PD)1 expression induced by HFD. A mechanistic study confirmed that BATF regulated fat accumulation by inhibiting PD1 expression and promoting energy metabolism. PD1 antibodies alleviated hepatic lipid deposition. In conclusion, we identified the regulatory role of BATF in hepatic lipid metabolism and that PD1 is a target for alleviation of NAFLD. This study provides new insights into the relationship between BATF, PD1, and NAFLD.
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Affiliation(s)
- Zhiwang Zhang
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Qichao Liao
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Tingli Pan
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Lin Yu
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Zupeng Luo
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Songtao Su
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Shi Liu
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Menglong Hou
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Yixing Li
- College of Animal Science and Technology, Guangxi UniversityNanningChina
| | - Turtushikh Damba
- School of Pharmacy, Mongolian National University of Medical SciencesUlan BatorMongolia
| | - Yunxiao Liang
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Lei Zhou
- Institute of Digestive Disease, Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous RegionNanningChina
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Ilieva M, Dao J, Miller HE, Madsen JH, Bishop AJR, Kauppinen S, Uchida S. Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease. Noncoding RNA 2022; 8:ncrna8040056. [PMID: 35893239 PMCID: PMC9332188 DOI: 10.3390/ncrna8040056] [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: 07/11/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/04/2022] Open
Abstract
The largest solid organ in humans, the liver, performs a variety of functions to sustain life. When damaged, cells in the liver can regenerate themselves to maintain normal liver physiology. However, some damage is beyond repair, which necessitates liver transplantation. Increasing rates of obesity, Western diets (i.e., rich in processed carbohydrates and saturated fats), and cardiometabolic diseases are interlinked to liver diseases, including non-alcoholic fatty liver disease (NAFLD), which is a collective term to describe the excess accumulation of fat in the liver of people who drink little to no alcohol. Alarmingly, the prevalence of NAFLD extends to 25% of the world population, which calls for the urgent need to understand the disease mechanism of NAFLD. Here, we performed secondary analyses of published RNA sequencing (RNA-seq) data of NAFLD patients compared to healthy and obese individuals to identify long non-coding RNAs (lncRNAs) that may underly the disease mechanism of NAFLD. Similar to protein-coding genes, many lncRNAs are dysregulated in NAFLD patients compared to healthy and obese individuals, suggesting that understanding the functions of dysregulated lncRNAs may shed light on the pathology of NAFLD. To demonstrate the functional importance of lncRNAs in the liver, loss-of-function experiments were performed for one NAFLD-related lncRNA, LINC01639, which showed that it is involved in the regulation of genes related to apoptosis, TNF/TGF, cytokine signaling, and growth factors as well as genes upregulated in NAFLD. Since there is no lncRNA database focused on the liver, especially NAFLD, we built a web database, LiverDB, to further facilitate functional and mechanistic studies of hepatic lncRNAs.
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Affiliation(s)
- Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark; (J.H.M.); (S.K.)
- Correspondence: (M.I.); (S.U.)
| | - James Dao
- Bioinformatics Research Network, Atlanta, GA 30317, USA; (J.D.); (H.E.M.)
| | - Henry E. Miller
- Bioinformatics Research Network, Atlanta, GA 30317, USA; (J.D.); (H.E.M.)
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA;
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Jens Hedelund Madsen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark; (J.H.M.); (S.K.)
| | - Alexander J. R. Bishop
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA;
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
- May’s Cancer Center, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark; (J.H.M.); (S.K.)
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark; (J.H.M.); (S.K.)
- Bioinformatics Research Network, Atlanta, GA 30317, USA; (J.D.); (H.E.M.)
- Correspondence: (M.I.); (S.U.)
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Metwally M, Berg T, Tsochatzis EA, Eslam M. Translation Reprogramming as a Novel Therapeutic Target in MAFLD. Adv Biol (Weinh) 2022; 6:e2101298. [PMID: 35240009 DOI: 10.1002/adbi.202101298] [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: 11/08/2021] [Revised: 01/19/2022] [Indexed: 01/27/2023]
Abstract
Approved pharmacotherapies for metabolic-dysfunction-associated fatty liver disease (MAFLD) are lacking. Novel approaches and therapeutic targets that are likely to translate to clinical benefit are required. Targeting components of the translation machinery hold promise as a novel therapeutic approach that can overcome the well-known disease heterogeneity, as dysregulation of mRNA translation is a common feature independent of the MAFLD drivers. In this perspective, recent advances in understanding the role of mRNA translation in MAFLD are discussed, with a particular focus on the potential implications and challenges to "translate" these findings to the clinic, and an overview of similar recent efforts in other diseases is provided.
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Affiliation(s)
- Mayada Metwally
- Department of Internal Medicine, Minia University, Minia, 61111, Egypt
| | - Thomas Berg
- Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, 04103, Leipzig, Germany
| | - Emmanuel A Tsochatzis
- UCL Institute for Liver and Digestive Health, Royal Free Hospital and UCL, London, NW3 2QG, UK
| | - Mohammed Eslam
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, New South Wales, 2145, Australia
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Welles JE, Lacko H, Kawasawa YI, Dennis MD, Jefferson LS, Kimball SR. An integrative approach to assessing effects of a short-term Western diet on gene expression in rat liver. Front Endocrinol (Lausanne) 2022; 13:1032293. [PMID: 36387860 PMCID: PMC9643360 DOI: 10.3389/fendo.2022.1032293] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/30/2022] [Accepted: 10/12/2022] [Indexed: 12/05/2022] Open
Abstract
Consumption of a diet rich in saturated fatty acids and carbohydrates contributes to the accumulation of fat in the liver and development of non-alcoholic steatohepatitis (NASH). Herein we investigated the hypothesis that short-term consumption of a high fat/sucrose Western diet (WD) alters the genomic and translatomic profile of the liver in association with changes in signaling through the protein kinase mTORC1, and that such alterations contribute to development of NAFLD. The results identify a plethora of mRNAs that exhibit altered expression and/or translation in the liver of rats consuming a WD compared to a CD. In particular, consumption of a WD altered the abundance and ribosome association of mRNAs involved in lipid and fatty acid metabolism, as well as those involved in glucose metabolism and insulin signaling. Hepatic mTORC1 signaling was enhanced when rats were fasted overnight and then refed in the morning; however, this effect was blunted in rats fed a WD as compared to a CD. Despite similar plasma insulin concentrations, fatty acid content was elevated in the liver of rats fed a WD as compared to a CD. We found that feeding had a significant positive effect on ribosome occupancy of 49 mRNAs associated with hepatic steatosis (e.g., LIPE, LPL), but this effect was blunted in the liver of rats fed a WD. In many cases, changes in ribosome association were independent of alterations in mRNA abundance, suggesting a critical role for diet-induced changes in mRNA translation in the expression of proteins encoded by those mRNAs. Overall, the findings demonstrate that short-term consumption of a WD impacts hepatic gene expression by altering the abundance of many mRNAs, but also causes wide-spread variation in mRNA translation that potentially contribute to development of hepatic steatosis.
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Affiliation(s)
- Jaclyn E. Welles
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, United States
| | - Holly Lacko
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, United States
| | - Yuka Imamura Kawasawa
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, United States
| | - Michael D. Dennis
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, United States
| | - Leonard S. Jefferson
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, United States
| | - Scot R. Kimball
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, United States
- *Correspondence: Scot R. Kimball,
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Huang T, Yu L, Pan H, Ma Z, Wu T, Zhang L, Liu K, Qi Q, Miao W, Song Z, Zhang H, Zhou L, Li Y. Integrated Transcriptomic and Translatomic Inquiry of the Role of Betaine on Lipid Metabolic Dysregulation Induced by a High-Fat Diet. Front Nutr 2021; 8:751436. [PMID: 34708066 PMCID: PMC8542779 DOI: 10.3389/fnut.2021.751436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
An excessive high-fat/energy diet is a major cause of obesity and linked complications, such as non-alcoholic fatty liver disease (NAFLD). Betaine has been shown to effectively improve hepatic lipid metabolism. However, the mechanistic basis for this improvement is largely unknown. Herein, integration of mRNA sequencing and ribosome footprints profiling (Ribo-seq) was used to investigate the means by which betaine alleviates liver lipid metabolic disorders induced by a high-fat diet. For the transcriptome, gene set enrichment analysis demonstrated betaine to reduce liver steatosis by up-regulation of fatty acid beta oxidation, lipid oxidation, and fatty acid catabolic processes. For the translatome, 574 differentially expressed genes were identified, 17 of which were associated with the NAFLD pathway. By combined analysis of transcriptome and translatome, we found that betaine had the greater effect on NAFLD at the translational level. Further, betaine decreased translational efficiency (TE) for IDI1, CYP51A1, TM7SF2, and APOA4, which are related to lipid biosynthesis. In summary, this study demonstrated betaine alleviating lipid metabolic dysfunction at the translational level. The transcriptome and translatome data integration approach used herein provides for a new understanding of the means by which to treat NAFLD.
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Affiliation(s)
- Tengda Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lin Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hongyuan Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zeqiang Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Tian Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lifang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Kang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qi Qi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Weiwei Miao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ziyi Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Haojie Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lei Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yixing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
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The use of ribosome-nascent chain complex-seq to reveal the translated mRNA profile and the role of ASN1 in resistance to Verticillium wilt in cotton. Genomics 2021; 113:3872-3880. [PMID: 34563615 DOI: 10.1016/j.ygeno.2021.09.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 08/19/2021] [Accepted: 09/18/2021] [Indexed: 11/22/2022]
Abstract
We combined traditional mRNA-seq and RNC-seq together to reveal post-transcriptional regulation events impacting gene expression and interactions between the serious fungal pathogen Verticillium dahliae and a susceptible host, Gossypium hirsutum TM-1. After screening the differentially expressed and translated genes, V. dahliae infection was observed to influence gene transcription and translation in its host. Interestingly, the asparagine synthase (ASN1) gene transcripts increased significantly with the increase of infection time, while the rate of ASN1 protein accumulation in host TM-1 was distinctly lower than that in resistant hosts. We knocked down the ASN1 gene in resistant plants (ZZM2), and found that Verticillium-resistance was significantly reduced upon knockdown of ASN1. Our study revealed both transcriptional and post-transcriptional regulation of gene expression in TM-1 cotton plants infected by V. dahliae, and showed that ASN1 functions in the V. dahliae resistance process. These insights support breeding of disease resistance in cotton.
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Zhang Z, Liao Q, Sun Y, Pan T, Liu S, Miao W, Li Y, Zhou L, Xu G. Lipidomic and Transcriptomic Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs. Front Nutr 2021; 8:667622. [PMID: 34055857 PMCID: PMC8154583 DOI: 10.3389/fnut.2021.667622] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/30/2021] [Indexed: 01/08/2023] Open
Abstract
Meat is an essential food, and pork is the largest consumer meat product in China and the world. Intramuscular fat has always been the basis for people to select and judge meat products. Therefore, we selected the Duroc, a western lean pig breed, and the Luchuan, a Chinese obese pig breed, as models, and used the longissimus dorsi muscle for lipidomics testing and transcriptomics sequencing. The purpose of the study was to determine the differences in intramuscular fat between the two breeds and identify the reasons for the differences. We found that the intramuscular fat content of Luchuan pigs was significantly higher than that of Duroc pigs. The triglycerides and diglycerides related to flavor were higher in Luchuan pigs compared to Duroc pigs. This phenotype may be caused by the difference in the expression of key genes in the glycerolipid metabolism signaling pathway.
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Affiliation(s)
- Zhiwang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qichao Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yu Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Tingli Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Siqi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Weiwei Miao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yixing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lei Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Gaoxiao Xu
- Teaching and Research Section of Biotechnology, Nanning University, Nanning, China
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