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Yang M, Zhang R, Liu X, Shi G, Liu H, Wang L, Hou X, Shi L, Wang L, Zhang L. Integrating genome-wide association study with RNA-seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs. Anim Genet 2023; 54:24-34. [PMID: 36305366 DOI: 10.1111/age.13270] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 01/07/2023]
Abstract
Increasing intramuscular fat (IMF) content can enhance the sensory quality of meat, including tenderness, juiciness, flavor, and color. Genome-wide association study and RNA-sequencing (RNA-seq) analysis were used to identify candidate IMF genes in Beijing Black pigs, a popular species among consumers in northern China. Two and three single nucleotide polymorphisms were significantly associated with IMF in SSC13 and SSC15 respectively. Solute carrier family 4 member 7 (SLC4A7) on SSC13 and insulin induced gene 2 (INSIG2), coiled-coil domain containing 93 (CCDC93), and diazepam binding inhibitor acyl-CoA binding protein (DBI) on SSC15 are good candidate genes in this population. Furthermore, RNA-seq analysis was performed between high and low IMF groups, and 534 differentially expressed genes were identified. In addition, based on differentially expressed genes, Kyoto Encyclopedia of Genes and Genomes analysis revealed that peroxisome proliferator-activated receptors and FoxO signaling pathway pathways might contribute to IMF. Moreover, the DBI gene was identified as a candidate for IMF both by genome-wide association study and RNA-seq analysis, suggesting that it might be a crucial candidate gene for influencing IMF in Beijing Black pigs.
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Affiliation(s)
- Man Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Run Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiance Liu
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Guohua Shi
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Hai Liu
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Ligang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhua Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijun Shi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longchao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Siddiqui H, Yevstigneyev N, Madani G, McCormick S. Approaches to Visualising Endocytosis of LDL-Related Lipoproteins. Biomolecules 2022; 12:biom12020158. [PMID: 35204658 PMCID: PMC8961563 DOI: 10.3390/biom12020158] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/20/2021] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Endocytosis is the process by which molecules are actively transported into cells. It can take on a variety of forms depending on the cellular machinery involved ranging from specific receptor-mediated endocytosis to the less selective and actin-driven macropinocytosis. The plasma lipoproteins, which deliver lipids and other cargo to cells, have been intensely studied with respect to their endocytic uptake. One of the first molecules to be visualised undergoing endocytosis via a receptor-mediated, clathrin-dependent pathway was low-density lipoprotein (LDL). The LDL molecule has subsequently been shown to be internalised through multiple endocytic pathways. Dissecting the pathways of lipoprotein endocytosis has been crucial to understanding the regulation of plasma lipid levels and how lipids enter cells in the arterial wall to promote atherosclerosis. It has also aided understanding of the dysregulation that occurs in plasma lipid levels when molecules involved in uptake are defective, as is the case in familial hypercholesterolemia (FH). The aim of this review is to outline the many endocytic pathways utilised for lipoprotein uptake. It explores the various experimental approaches that have been applied to visualise lipoprotein endocytosis with an emphasis on LDL and its more complex counterpart, lipoprotein(a) [Lp(a)]. Finally, we look at new developments in lipoprotein visualisation that hold promise for scrutinising endocytic pathways to finer detail in the future.
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Affiliation(s)
- Halima Siddiqui
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (H.S.); (N.Y.); (G.M.)
- HeartOtago, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Nikita Yevstigneyev
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (H.S.); (N.Y.); (G.M.)
- HeartOtago, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Golnoush Madani
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (H.S.); (N.Y.); (G.M.)
- HeartOtago, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Sally McCormick
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (H.S.); (N.Y.); (G.M.)
- HeartOtago, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
- Correspondence:
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Ahi EP, Lecaudey LA, Ziegelbecker A, Steiner O, Goessler W, Sefc KM. Expression levels of the tetratricopeptide repeat protein gene ttc39b covary with carotenoid-based skin colour in cichlid fish. Biol Lett 2020; 16:20200629. [PMID: 33236977 PMCID: PMC7728679 DOI: 10.1098/rsbl.2020.0629] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Carotenoid pigments play a major role in animal body colouration, generating strong interest in the genes involved in the metabolic processes that lead from their dietary uptake to their storage in the integument. Here, we used RNA sequencing (RNA-Seq) to test for differentially expressed genes in a taxonomically replicated design using three pairs of related cichlid fish taxa from the genera Tropheus and Aulonocara. Within each pair, taxa differed in terms of red and yellow body colouration, and high‐performance liquid chromatography (HPLC) analyses of skin extracts revealed different carotenoid profiles and concentrations across the studied taxa. Five genes were differentially expressed in all three yellow–red skin contrasts (dhrsx, nlrc3, tcaf2, urah and ttc39b), but only the tetratricopeptide repeat protein-coding gene ttc39b, whose gene product is linked to mammalian lipid metabolism, was consistently expressed more highly in the red skin samples. The RNA-Seq results were confirmed by quantitative PCR. We propose ttc39b as a compelling candidate gene for variation in animal carotenoid colouration. Since differential expression of ttc39b was correlated with the presence/absence of yellow carotenoids in a previous study, we suggest that ttc39b is more likely associated with the concentration of total carotenoids than with the metabolic formation of red carotenoids.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria.,Department of Comparative Physiology, Uppsala University, Norbyvägen 18A, SE-75 236 Uppsala, Sweden
| | - Laurène A Lecaudey
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria.,Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | | | - Oliver Steiner
- Institute of Chemistry, University of Graz, Universitätsplatz 1, A-8010 Graz, Austria
| | - Walter Goessler
- Institute of Chemistry, University of Graz, Universitätsplatz 1, A-8010 Graz, Austria
| | - Kristina M Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
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Le R, Abbas M, McIntyre AD, Hegele RA. Severe Combined Dyslipidemia With a Complex Genetic Basis. J Investig Med High Impact Case Rep 2020; 7:2324709619877050. [PMID: 31538826 PMCID: PMC6755624 DOI: 10.1177/2324709619877050] [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] [Indexed: 12/16/2022] Open
Abstract
Background. Familial dysbetalipoproteinemia (also known as type 3 hyperlipoproteinemia) is typically associated with homozygosity for the apolipoprotein E2 isoform, but also sometimes with dominant rare missense variants in the APOE gene. Patients present with roughly equimolar elevations of cholesterol and triglyceride (TG) due to pathologic accumulation of remnant lipoprotein particles. Clinical features include tuberoeruptive xanthomas, palmar xanthomas, and premature vascular disease. Case. A 48-year-old male presented with severe combined dyslipidemia: total cholesterol and TG were 11.5 and 21.4 mmol/L, respectively. He had dyslipidemia since his early 20s, with tuberous xanthomas on his elbows and knees. His body mass index was 42 kg/m2. He also had treated hypertension, mild renal impairment, and a history of gout. He had no history of cardiovascular disease, peripheral arterial disease, or pancreatitis. Multiple medications had been advised including rosuvastatin, ezetimibe, fenofibrate, and alirocumab, but his lipid levels were never adequately controlled. Genetic Analysis. Targeted next-generation sequencing identified (1) the APOE E2/E2 homozygous genotype classically described with familial dysbetalipoproteinemia; (2) in addition, one APOE E2 allele contained the rare heterozygous missense variant p.G145D, previously termed apo E-Bethesda; (3) a rare heterozygous APOC2 nonsense variant p.Q92X; and (4) a high polygenic risk score for TG levels (16 out of 28 TG-raising alleles) at the 82nd percentile for age and sex. Conclusion. The multiple genetic "hits" on top of the classical APOE E2/E2 genotype likely explain the more severe dyslipidemia and refractory clinical phenotype.
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Affiliation(s)
- Ryan Le
- Western University, London, Ontario, Canada
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Genes Potentially Associated with Familial Hypercholesterolemia. Biomolecules 2019; 9:biom9120807. [PMID: 31795497 PMCID: PMC6995538 DOI: 10.3390/biom9120807] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/24/2019] [Accepted: 11/26/2019] [Indexed: 12/21/2022] Open
Abstract
This review addresses the contribution of some genes to the phenotype of familial hypercholesterolemia. At present, it is known that the pathogenesis of this disease involves not only a pathological variant of low-density lipoprotein receptor and its ligands (apolipoprotein B, proprotein convertase subtilisin/kexin type 9 or low-density lipoprotein receptor adaptor protein 1), but also lipids, including sphingolipids, fatty acids, and sterols. The genetic cause of familial hypercholesterolemia is unknown in 20%–40% of the cases. The genes STAP1 (signal transducing adaptor family member 1), CYP7A1 (cytochrome P450 family 7 subfamily A member 1), LIPA (lipase A, lysosomal acid type), ABCG5 (ATP binding cassette subfamily G member 5), ABCG8 (ATP binding cassette subfamily G member 8), and PNPLA5 (patatin like phospholipase domain containing 5), which can cause aberrations of lipid metabolism, are being evaluated as new targets for the diagnosis and personalized management of familial hypercholesterolemia.
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Abstract
PURPOSE OF REVIEW Residual cardiovascular disease risk and increasing metabolic syndrome risk underscores a need for novel therapeutics targeting lipid metabolism in humans. Unbiased human genetic screens have proven powerful in identifying novel genomic loci, and this review discusses recent developments in such discovery. RECENT FINDINGS Recent human genome-wide association studies have been completed in incredibly large, detailed cohorts, allowing for the identification of more than 300 genomic loci that participate in the regulation of plasma lipid metabolism. However, the discovery of these loci has greatly outpaced the elucidation of the underlying functional mechanisms. The identification of novel roles for long noncoding RNAs, such as CHROME, LeXis, and MeXis, in lipid metabolism suggests that noncoding RNAs should be included in the functional translation of GWAS loci. SUMMARY Unbiased genetic studies appear to have unearthed a great deal of novel biology with respect to lipid metabolism, yet translation of these findings into actionable mechanisms has been slow. Increased focus on the translation, rather than the discovery, of these loci, with new attention paid to lncRNAs, can help spur the development of novel therapeutics targeting lipid metabolism.
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Affiliation(s)
- Elizabeth E. Ha
- Cardiometabolic Genomics Program, Division of Cardiology, Department of
Medicine, Columbia University, New York, NY, 10032
| | - Andrew G. Van Camp
- Cardiometabolic Genomics Program, Division of Cardiology, Department of
Medicine, Columbia University, New York, NY, 10032
| | - Robert C. Bauer
- Cardiometabolic Genomics Program, Division of Cardiology, Department of
Medicine, Columbia University, New York, NY, 10032
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Wang W, Zhang ZZ, Wu Y, Wang RQ, Chen JW, Chen J, Zhang Y, Chen YJ, Geng M, Xu ZD, Dai M, Li JH, Pan LL. (-)-Epigallocatechin-3-Gallate Ameliorates Atherosclerosis and Modulates Hepatic Lipid Metabolic Gene Expression in Apolipoprotein E Knockout Mice: Involvement of TTC39B. Front Pharmacol 2018; 9:195. [PMID: 29593532 PMCID: PMC5854642 DOI: 10.3389/fphar.2018.00195] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/21/2018] [Indexed: 12/22/2022] Open
Abstract
Background: Aberrant chronic inflammation and excess accumulation of lipids play a pivotal role in the occurrence and progression of atherosclerosis. (–)-Epigallocatechin-3-gallate (EGCG), the major catechins in green tea, displayed anti-atherosclerotic properties in vivo and in vitro. However, the effects and underlying mechanism of EGCG on atherosclerosis remain unclear. Methods: Male apolipoprotein E-knockout (ApoE-/-) mice (7 weeks old) fed with high-fat diet (HFD) were treated with normal saline or EGCG (40 mg/kg/d, i.g.) for 18 weeks. Atherosclerotic plaque and liver lipid accumulation were measured by Oil Red staining. Plasma lipids and cytokines were detected using commercial kits. The expression of protein and mRNA was analyzed by western blot and quantitative real-time reverse transcription-polymerase chain reaction, respectively. Results: EGCG administration markedly attenuated atherosclerotic plaque formation in HFD-fed ApoE-/- mice, which were accompanied by increased plasma interleukin-10 (IL-10) level and decreased plasma IL-6 and tumor necrosis factor-α (TNF-α) levels. In addition, EGCG modulated high-fat-induced dyslipidemia, evidencing by decreased total cholesterol (TC) and low-density lipoprotein levels and increased high-density lipoprotein level. Meanwhile, EGCG treatment alleviated high-fat-mediated liver lipid accumulation and decreased liver TC and triglyceride. Mechanistically, EGCG significantly modulated high-fat-induced hepatic tetratricopeptide repeat domain protein 39B (TTC39B) expression and its related genes (Lxrβ, Abcg5, Abcg8, Abca1, Srebf1, Scd1, Scd2, Fas, Elovl5, Mylip) expression in liver from ApoE-/- mice. Notably, EGCG remarkably induced hepatic liver X receptor α (LXRα) and LXRβ expression and inhibited both precursor and mature sterol regulatory element binding transcription factor-1 (SREBP-1) expression. Conclusion: Taken together, our data for the first time suggested that TTC39B was involved in EGCG-mediated anti-atherosclerotic effects through modulation of LXR/SREBP-1 pathway.
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Affiliation(s)
- Wei Wang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Yan Wu
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Ru-Qing Wang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Jin-Wu Chen
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Jing Chen
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Yan Zhang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Ya-Jun Chen
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Ming Geng
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Zhong-Dong Xu
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Min Dai
- Anhui Key Laboratory for Research and Development of Traditional Chinese Medicine, Key Laboratory of Xin'an Medicine, Ministry of Education, School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Jin-Hua Li
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Li-Long Pan
- School of Medicine, Jiangnan University, Wuxi, China
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