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Duan S, Li H, Wang Z, Li J, Huang W, Fang Z, Li C, Zeng Z, Sun B, Liu Y. Tibetan tea consumption prevents obesity by modulating the cellular composition and metabolic reprogramming of white adipose tissue. Food Funct 2024; 15:208-222. [PMID: 38047533 DOI: 10.1039/d3fo03506a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Obesity, a global health concern, is linked with numerous metabolic and inflammatory disorders. Tibetan tea, a traditional Chinese beverage rich in theabrownin, is investigated in this study for its potential anti-obesity effects. Our work demonstrates that Tibetan tea consumption in C57BL/6J mice significantly mitigates obesity-related phenotypic changes without altering energy intake. Computational prediction revealed that Tibetan tea consumption reconstructs gene expression in white adipose tissue (WAT), promoting lipid catabolism and thereby increasing energy expenditure. We also note that Tibetan tea suppresses inflammation in WAT, reducing adipocyte hyperplasia and immune cell infiltration. Furthermore, Tibetan tea induces profound metabolic reprogramming, influencing amino acid metabolic pathways, specifically enhancing glutamine synthesis, which in turn suppresses pro-inflammatory chemokine production. These findings highlight Tibetan tea as a potential candidate in obesity prevention, providing a nuanced understanding of its capacity to modulate the cellular composition and metabolic landscape of WAT.
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Affiliation(s)
- Songqi Duan
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Hongyu Li
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Ziqi Wang
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Junqi Li
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Weimin Huang
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Zhengfeng Fang
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Cheng Li
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Zhen Zeng
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Baofa Sun
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuntao Liu
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
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2
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Islam S, Zhang D, Ho K, Divers J. Racial Disparities in Hospitalization Rates During Long-Term Follow-Up After Deceased-Donor Kidney Transplantation. J Racial Ethn Health Disparities 2023:10.1007/s40615-023-01847-4. [PMID: 37930581 DOI: 10.1007/s40615-023-01847-4] [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: 05/17/2023] [Revised: 08/23/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
OBJECTIVE To compare hospitalization rates between African American (AA) and European American (EA) deceased-donor (DD) kidney transplant (KT) recipients during over a10-year period. METHOD Data from the Scientific Registry of Transplant Recipients and social determinants of health (SDoH), measured by the Social Deprivation Index, were used. Hospitalization rates were estimated for kidney recipients from AA and EA DDs who had one kidney transplanted into an AA and one into an EA, leading to four donor/recipient pairs (DRPs): AA/AA, AA/EA, EA/AA, and EA/EA. Poisson-Gamma models were fitted to assess post-transplant hospitalizations. RESULT Unadjusted hospitalization rates (95% confidence interval) were higher among all DRP involving AA, 131.1 (122.5, 140.3), 134.8 (126.3, 143.8), and 102.4 (98.9, 106.0) for AA/AA, AA/EA, and EA/AA, respectively, compared to 97.1 (93.7, 100.6) per 1000 post-transplant person-years for EA/EA pairs. Multivariable analysis showed u-shaped relationships across SDoH levels within each DRP, but findings varied depending on recipients' race, i.e., AA recipients in areas with the worst SDoH had higher hospitalization rates. However, EA recipients in areas with the best SDoH had higher hospitalization rates than their counterparts. CONCLUSIONS Relationship between healthcare utilization and SDoH depends on DRP, with higher hospitalization rates among AA recipients living in areas with the worst SDoH and among EA recipients in areas with the best SDoH profiles. SDoH plays an important role in driving disparities in hospitalizations after kidney transplantation.
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Affiliation(s)
- Shahidul Islam
- Department of Foundations of Medicine, Division of Health Services Research, NYU Grossman Long Island School of Medicine, 101 Mineola Blvd, Mineola, NY, 11501, USA.
- NYU Grossman Long Island School of Medicine, Mineola, NY, USA.
| | - Donglan Zhang
- Department of Foundations of Medicine, Division of Health Services Research, NYU Grossman Long Island School of Medicine, 101 Mineola Blvd, Mineola, NY, 11501, USA
- NYU Grossman Long Island School of Medicine, Mineola, NY, USA
| | - Kimberly Ho
- NYU Grossman Long Island School of Medicine, Mineola, NY, USA
| | - Jasmin Divers
- Department of Foundations of Medicine, Division of Health Services Research, NYU Grossman Long Island School of Medicine, 101 Mineola Blvd, Mineola, NY, 11501, USA
- NYU Grossman Long Island School of Medicine, Mineola, NY, USA
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3
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Zhu C, Qi Y, Wang X, Mi B, Cui C, Chen S, Zhao Z, Zhao F, Liu X, Wang J, Shi B, Hu J. Variation in Acetyl-CoA Carboxylase Beta Gene and Its Effect on Carcass and Meat Traits in Gannan Yaks. Int J Mol Sci 2023; 24:15488. [PMID: 37895167 PMCID: PMC10607073 DOI: 10.3390/ijms242015488] [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: 06/25/2023] [Revised: 09/12/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Acetyl-CoA carboxylase beta (ACACB) is a functional candidate gene that impacts fat deposition. In the present study, we sequenced exon 37-intron 37, exon 46-intron 46, and intron 47 of yak ACACB using hybrid pool sequencing to search for variants and genotyped the gene in 593 Gannan yaks via Kompetitive allele-specific polymerase chain (KASP) reaction to determine the effect of ACACB variants on carcass and meat quality traits. Seven single nucleotide polymorphisms were detected in three regions. Eight effective haplotypes and ten diplotypes were constructed. Among them, a missense variation g.50421 A > G was identified in exon 37 of ACACB, resulting in an amino acid shift from serine to glycine. Correlation analysis revealed that this variation was associated with the cooking loss rate and yak carcass weight (p = 0.024 and 0.012, respectively). The presence of haplotypes H5 and H6 decreased Warner-Bratzler shear force (p = 0.049 and 0.006, respectively), whereas that of haplotypes H3 and H4 increased cooking loss rate and eye muscle area (p = 0.004 and 0.034, respectively). Moreover, the presence of haplotype H8 decreased the drip loss rate (p = 0.019). The presence of one and two copies of haplotypes H1 and H8 decreased the drip loss rate (p = 0.028 and 0.004, respectively). However, haplotype H1 did not decrease hot carcass weight (p = 0.011), whereas H3 increased the cooking loss rate (p = 0.007). The presence of one and two copies of haplotype H6 decreased Warner-Bratzler shear force (p = 0.014). The findings of the present study suggest that genetic variations in ACACB can be a preferable biomarker for improving yak meat quality.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bingang Shi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (C.Z.); (Y.Q.); (X.W.); (B.M.); (C.C.); (S.C.); (Z.Z.); (F.Z.); (X.L.); (J.W.)
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (C.Z.); (Y.Q.); (X.W.); (B.M.); (C.C.); (S.C.); (Z.Z.); (F.Z.); (X.L.); (J.W.)
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4
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Cheshmeh S, Nachvak SM, Hojati N, Elahi N, Heidarzadeh‐Esfahani N, Saber A. The effects of breastfeeding and formula feeding on the metabolic factors and the expression level of obesity and diabetes-predisposing genes in healthy infants. Physiol Rep 2022; 10:e15469. [PMID: 36200185 PMCID: PMC9535349 DOI: 10.14814/phy2.15469] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
Diabetes mellitus (DM) and obesity are common illnesses characterized by glucose metabolism issues and excessive weight gain. Breastfeeding is the best way to feed a newborn up to 6 months old and it has been shown to reduce the risk of diabetes and obesity later in life due to its nutritional properties. The purpose of this study was to investigate the effects of breastfeeding, formula feeding, and formula-plus breastfeeding (mix-feeding) on the anthropometric indices, metabolic variables, and the expression level of obesity and diabetes-predisposing genes of healthy infants. A total of 150 healthy infants were enrolled in this cross-sectional study. All infants (aged 24 months) were divided into three groups based on the type of feeding, breastfeeding, formula feeding, and mix-feeding. The anthropometric indices, glycemic indexes, lipid profile, and the expression levels of acetyl-coenzyme A carboxylase beta (ACACB), brain-derived neurotrophic factor (BDNF), liver X receptor α (LXR-α), peroxisome proliferator-activated receptor γ (PPAR-γ), and phosphatase and tensin homolog (PTEN) genes were measured in all infants using reverse transcription-polymerase chain reaction (RT-PCR) method. The anthropometric indices including weight, height, head circumference, insulin, total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) were lower in the breastfeeding infants in comparison to other groups. As well, the expression level of the ACACB gene was significantly downregulated in breastfeeding infants, while the PPAR-γ gene was significantly upregulated, but the expression levels of LXR- α, PTEN and BDNF did not change significantly across groups. Breastfeeding compared to formula feeding had positive effects on anthropometric indices, metabolic variables, and diabetes-predisposing genes.
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Affiliation(s)
- Sahar Cheshmeh
- Department of Nutritional Sciences, School of Nutritional Sciences and Food TechnologyKermanshah University of Medical SciencesKermanshahIran
- Student Research Committee, School of Nutritional Sciences and Food TechnologyKermanshah University of Medical SciencesKermanshahIran
| | - Seyed Mostafa Nachvak
- Department of Nutritional Sciences, School of Nutritional Sciences and Food TechnologyKermanshah University of Medical SciencesKermanshahIran
| | - Niloofar Hojati
- Department of Nutritional Sciences, School of Nutritional Sciences and Food TechnologyKermanshah University of Medical SciencesKermanshahIran
- Student Research Committee, School of Nutritional Sciences and Food TechnologyKermanshah University of Medical SciencesKermanshahIran
| | - Negin Elahi
- Department of Nutritional Sciences, School of Nutritional Sciences and Food TechnologyKermanshah University of Medical SciencesKermanshahIran
- Student Research Committee, School of Nutritional Sciences and Food TechnologyKermanshah University of Medical SciencesKermanshahIran
| | - Neda Heidarzadeh‐Esfahani
- Department of Nutritional Sciences, School of Nutritional Sciences and Food TechnologyKermanshah University of Medical SciencesKermanshahIran
- Student Research Committee, School of Nutritional Sciences and Food TechnologyKermanshah University of Medical SciencesKermanshahIran
| | - Amir Saber
- Department of Nutritional Sciences, School of Nutritional Sciences and Food TechnologyKermanshah University of Medical SciencesKermanshahIran
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Peng G, Zhu C, Sun Q, Li J, Chen Y, Guo Y, Ji H, Yang F, Dong W. Testicular miRNAs and tsRNAs provide insight into gene regulation during overwintering and reproduction of Onychostoma macrolepis. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:481-499. [PMID: 35595880 DOI: 10.1007/s10695-022-01078-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
The late overwintering period and breeding period are two important developmental stages of testis in Onychostoma macrolepis. Small non-coding RNAs (sncRNAs) are well-known regulators of biological processes associated with numerous biological processes. This study aimed to elucidate the roles of four sncRNA classes (microRNAs [miRNAs], Piwi-interacting RNAs [piRNAs], tRNA-derived small RNAs [tsRNAs], and rRNA-derived small RNAs [rsRNAs]) across testes in the late overwintering period (in March) and breeding period (in June) by high-throughput sequencing. The testis of O. macrolepis displayed the highest levels of piRNAs and lowest levels of rsRNAs. Compared with miRNAs and tsRNAs in June, tsRNAs in March had a higher abundance, while miRNAs in March had a much lower abundance. Bioinformatics analysis identified 1,362 and 1,340 differentially expressed miRNAs and tsRNAs, respectively. Further analysis showed that miR-200-1, miR-143-1, tRFi-Lys-CTT-1, and tRFi-Glu-CTC-1 could play critical roles during the overwintering and breeding periods. Our findings provided an unprecedented insight to reveal the epigenetic mechanism underlying the overwintering and reproduction process of male O. macrolepis.
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Affiliation(s)
- Guofan Peng
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
- Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Chao Zhu
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
- Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Qingfang Sun
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Jincan Li
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Yining Chen
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Yingjie Guo
- Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
- College of Forestry, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Hong Ji
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Fangxia Yang
- Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China.
- College of Forestry, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China.
| | - Wuzi Dong
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China.
- Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China.
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6
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Bao G, Zhao F, Wang J, Liu X, Hu J, Shi B, Wen Y, Zhao L, Luo Y, Li S. Characterization of the circRNA–miRNA–mRNA Network to Reveal the Potential Functional ceRNAs Associated With Dynamic Changes in the Meat Quality of the Longissimus Thoracis Muscle in Tibetan Sheep at Different Growth Stages. Front Vet Sci 2022; 9:803758. [PMID: 35433904 PMCID: PMC9011000 DOI: 10.3389/fvets.2022.803758] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/23/2022] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) have a regulatory role in animal skeletal muscle development. In this study, RNA sequencing was performed to reveal the temporal regularity of circRNA expression and the effect of the circRNA–miRNA–mRNA ceRNA regulatory network on the meat quality of longissimus thoracis (LT) muscle in Tibetan sheep at different growth stages (4 months old, 4 m; 1.5 years old, 1.5 y; 3.5 years old, 3.5 y; 6 years old, 6 y). There were differences in the carcass performance and meat quality of Tibetan sheep at different ages. Especially, the meat tenderness significantly decreased (p < 0.05) with the increase of age. GO functional enrichment indicated that the source genes of the DE circRNAs were mainly involved in the protein binding, and myofibril and organelle assembly. Moreover, there was a significant KEGG enrichment in the adenosine 5′-monophosphate (AMP)-activated protein kinase (AMPK) signaling pathway, as well as the calcium signaling pathway, regulating the pluripotency of the stem cells. The circRNA–miRNA–mRNA ceRNA interaction network analysis indicated that circRNAs such as circ_000631, circ_000281, and circ_003400 combined with miR-29-3p and miR-185-5p regulate the expression of LEP, SCD, and FASN related to the transformation of muscle fiber types in the AMPK signaling pathway. The oxidized muscle fibers were transformed into the glycolytic muscle fibers with the increase of age, the content of intramuscular fat (IMF) was lowered, and the diameter of the muscle fiber was larger in the glycolytic muscle fibers, ultimately increasing the meat tenderness. The study revealed the role of the circRNAs in the transformation of skeletal muscle fiber types in Tibetan sheep and its influence on meat quality. It improves our understanding of the role of circRNAs in Tibetan sheep muscle development.
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Affiliation(s)
- Gaoliang Bao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bingang Shi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuliang Wen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Li Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Zheng J, Du M, Zhang J, Liang Z, Ahmad AA, Shen J, Salekdeh GH, Ding X. Transcriptomic and Metabolomic Analyses Reveal Inhibition of Hepatic Adipogenesis and Fat Catabolism in Yak for Adaptation to Forage Shortage During Cold Season. Front Cell Dev Biol 2022; 9:759521. [PMID: 35111749 PMCID: PMC8802892 DOI: 10.3389/fcell.2021.759521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022] Open
Abstract
Animals have adapted behavioral and physiological strategies to conserve energy during periods of adverse conditions. Hepatic glucose is one such adaptation used by grazing animals. While large vertebrates have been shown to have feed utilization and deposition of nutrients—fluctuations in metabolic rate—little is known about the regulating mechanism that controls hepatic metabolism in yaks under grazing conditions in the cold season. Hence, the objective of this research was to integrate transcriptomic and metabolomic data to better understand how the hepatic responds to chronic nutrient stress. Our analyses indicated that the blood parameters related to energy metabolism (glucose, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, lipoprotein lipase, insulin, and insulin-like growth factor 1) were significantly (p < 0.05) lower in the cold season. The RNA-Seq results showed that malnutrition inhibited lipid synthesis (particularly fatty acid, cholesterol, and steroid synthesis), fatty acid oxidation, and lipid catabolism and promoted gluconeogenesis by inhibiting the peroxisome proliferator-activated receptor (PPAR) and PI3K-Akt signaling pathways. For metabolite profiles, 359 metabolites were significantly altered in two groups. Interestingly, the cold season group remarkably decreased glutathione and phosphatidylcholine (18:2 (2E, 4E)/0:0). Moreover, integrative analysis of the transcriptome and metabolome demonstrated that glycolysis or gluconeogenesis, PPAR signaling pathway, fatty acid biosynthesis, steroid biosynthesis, and glutathione metabolism play an important role in the potential relationship between differential expression genes and metabolites. The reduced lipid synthesis, fatty acid oxidation, and fat catabolism facilitated gluconeogenesis by inhibiting the PPAR and PI3K-Akt signaling pathways to maintain the energy homeostasis of the whole body in the yak, thereby coping with the shortage of forages and adapting to the extreme environment of the Qinghai-Tibetan Plateau (QTP).
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Affiliation(s)
- Juanshan Zheng
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mei Du
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianbo Zhang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zeyi Liang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Anum Ali Ahmad
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jiahao Shen
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
- *Correspondence: Ghasem Hosseini Salekdeh, ; Xuezhi Ding,
| | - Xuezhi Ding
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- *Correspondence: Ghasem Hosseini Salekdeh, ; Xuezhi Ding,
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Cheng Y, Song M, Zhu Q, Azad MAK, Gao Q, Kong X. Impacts of Betaine Addition in Sow and Piglet's Diets on Growth Performance, Plasma Hormone, and Lipid Metabolism of Bama Mini-Pigs. Front Nutr 2022; 8:779171. [PMID: 35004811 PMCID: PMC8733558 DOI: 10.3389/fnut.2021.779171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/15/2021] [Indexed: 11/23/2022] Open
Abstract
The present study evaluated the effects of betaine addition in sow and piglet's diets on growth performance, plasma hormone, and lipid metabolism of Bama mini-pigs. A total of 26 pregnant Bama mini-pigs and 104 weaned piglets were selected and divided into different dietary treatment groups (details in “Materials and Methods”). Blood and muscle samples were collected at 65-, 95-, and 125-day-old, respectively. The results showed that betaine addition in sow-offspring diets increased (P < 0.05) the body weight at 125-day-old, average daily gain from 35- to 65-day-old, and average daily feed intake at 35–65 and 35–95 days old of pigs compared with the control group. Betaine addition in sow-offspring diets increased (P < 0.05) the plasma gastrin level at 95-day-old, while betaine addition in sow diets decreased (P < 0.05) the plasma peptide YY and leptin levels at 65-day-old pigs. In the longissimus dorsi muscle of pigs, betaine addition in sow and sow-offspring diets increased (P < 0.05) the C12:0 content at 65-day-old while decreased at 95-day-old. Moreover, betaine addition in sow-offspring diets increased the C24:0 content and decreased the C18:1n9t content at 125-day-old (P < 0.05). In the biceps femoris muscle, the contents of C12:0 at 65-day-old and C20:4n6 at 125-day-old were decreased (P < 0.05) after the betaine addition in both sow and piglet's diets. In addition, betaine addition in sow diets decreased (P < 0.05) the C20:0 content at 125-day-old, while betaine addition in sow-offspring diets increased the C18:3n6 and decreased C24:0 contents at 65-day-old pigs (P < 0.05). In the psoas major muscle, betaine addition in sow and sow-offspring diets decreased (P < 0.05) the contents of C18:1n9t at 65-day-old and C20:1 at 95-day-old, while betaine addition in sow diets decreased (P < 0.05) the intramuscular fat content at 125-day-old. Moreover, betaine addition in sow-offspring diets was also associated with muscle lipid deposition and metabolisms by regulating the gene expressions related to fatty acid metabolism. These findings suggested that betaine addition in sow-offspring diets could improve the growth performance, whereas betaine addition in both sow and sow-offspring diets could enhance lipid quality by altering plasma hormone level and fatty acid composition and regulating the gene expressions related to fatty acid metabolism.
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Affiliation(s)
- Yating Cheng
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mingtong Song
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Qian Zhu
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Md Abul Kalam Azad
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiankun Gao
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Xiangfeng Kong
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.,University of Chinese Academy of Sciences, Beijing, China.,Research Center of Mini-Pig, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang, China
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9
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Xiong L, Pei J, Kalwar Q, Wu X, Yan P, Guo X. Fat deposition in yak during different phenological seasons. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Machado RA, Martelli-Junior H, Reis SRDA, Küchler EC, Scariot R, das Neves LT, Coletta RD. Identification of Novel Variants in Cleft Palate-Associated Genes in Brazilian Patients With Non-syndromic Cleft Palate Only. Front Cell Dev Biol 2021; 9:638522. [PMID: 34307341 PMCID: PMC8297955 DOI: 10.3389/fcell.2021.638522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/30/2021] [Indexed: 12/17/2022] Open
Abstract
The identification of genetic risk factors for non-syndromic oral clefts is of great importance for better understanding the biological processes related to this heterogeneous and complex group of diseases. Herein we applied whole-exome sequencing to identify potential variants related to non-syndromic cleft palate only (NSCPO) in the multiethnic Brazilian population. Thirty NSCPO samples and 30 sex- and genetic ancestry-matched healthy controls were pooled (3 pools with 10 samples for each group) and subjected to whole-exome sequencing. After filtering, the functional affects, individually and through interactions, of the selected variants and genes were assessed by bioinformatic analyses. As a group, 399 variants in 216 genes related to palatogenesis/cleft palate, corresponding to 6.43%, were exclusively identified in the NSCPO pools. Among those genes are 99 associated with syndromes displaying cleft palate in their clinical spectrum and 92 previously related to cleft lip palate. The most significantly biological processes and pathways overrepresented in the NSCPO-identified genes were associated with the folic acid metabolism, highlighting the interaction between LDL receptor-related protein 6 (LRP6) and 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) that interconnect two large networks. This study yields novel data on characterization of specific variants and complex processes and pathways related to NSCPO, including many variants in genes of the folate/homocysteine pathway, and confirms that variants in genes related to syndromic cleft palate and cleft lip-palate may cause NSCPO.
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Affiliation(s)
- Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas (FOP), Piracicaba, Brazil.,Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil
| | - Hercílio Martelli-Junior
- Stomatology Clinic, School of Dental, State University of Montes Claros, Montes Claros, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, School of Dental, UNIFENAS - Universidade José do Rosario Vellano, Alfenas, Brazil
| | | | | | - Rafaela Scariot
- Department of Oral and Maxillofacial Surgery, School of Health Science, Federal University of Paraná, Curitiba, Brazil
| | - Lucimara Teixeira das Neves
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil.,Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo (FOB), Bauru, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas (FOP), Piracicaba, Brazil
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11
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Li P, Xia Z, Kong W, Wang Q, Zhao Z, Arnold A, Xu Q, Xu J. Exogenous L-carnitine ameliorates burn-induced cellular and mitochondrial injury of hepatocytes by restoring CPT1 activity. Nutr Metab (Lond) 2021; 18:65. [PMID: 34167568 PMCID: PMC8223334 DOI: 10.1186/s12986-021-00592-x] [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: 01/13/2021] [Accepted: 06/12/2021] [Indexed: 12/24/2022] Open
Abstract
Background Impaired hepatic fatty acid metabolism and persistent mitochondrial dysfunction are phenomena commonly associated with liver failure. Decreased serum levels of L-carnitine, a amino acid derivative involved in fatty-acid and energy metabolism, have been reported in severe burn patients. The current study aimed to evaluate the effects of L-carnitine supplementation on mitochondrial damage and other hepatocyte injuries following severe burns and the related mechanisms. Methods Serum carnitine and other indicators of hepatocytic injury, including AST, ALT, LDH, TG, and OCT, were analyzed in severe burn patients and healthy controls. A burn model was established on the back skin of rats; thereafter, carnitine was administered, and serum levels of the above indicators were evaluated along with Oil Red O and TUNEL staining, transmission electron microscopy, and assessment of mitochondrial membrane potential and carnitine palmitoyltransferase 1 (CPT1) activity and expression levels in the liver. HepG2 cells pretreated with the CPT1 inhibitor etomoxir were treated with or without carnitine for 24 h. Next, the above indicators were examined, and apoptotic cells were analyzed via flow cytometry. High-throughput sequencing of rat liver tissues identified several differentially expressed genes (Fabp4, Acacb, Acsm5, and Pnpla3) were confirmed using RT-qPCR. Results Substantially decreased serum levels of carnitine and increased levels of AST, ALT, LDH, and OCT were detected in severe burn patients and the burn model rats. Accumulation of TG, evident mitochondrial shrinkage, altered mitochondrial membrane potential, decreased ketogenesis, and reduced CPT1 activity were detected in the liver tissue of the burned rats. Carnitine administration recovered CPT1 activity and improved all indicators related to cellular and fatty acid metabolism and mitochondrial injury. Inhibition of CPT1 activity with etomoxir induced hepatocyte injuries similar to those in burn patients and burned rats; carnitine supplementation restored CPT1 activity and ameliorated these injuries. The expression levels of the differentially expressed genes Fabp4, Acacb, Acsm5, and Pnpla3 in the liver tissue from burned rats and etomoxir-treated hepatocytes were also restored by treatment with exogenous carnitine. Conclusion Exogenous carnitine exerts protective effects against severe burn-induced cellular, fatty-acid metabolism, and mitochondrial dysfunction of hepatocytes by restoring CPT1 activity. Supplementary Information The online version contains supplementary material available at 10.1186/s12986-021-00592-x.
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Affiliation(s)
- Pengtao Li
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.,Department of Immunology, School of Basic Medical Sciences of Anhui Medical University, No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Zhengguo Xia
- Department of Wound Repair and Plastic and Aesthetic Surgery, The Fourth Affiliated Hospital of Anhui Medical University, No. 100 Huaihai Road, Xinzhan District, China
| | - Weichang Kong
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
| | - Qiong Wang
- Department of Immunology, School of Basic Medical Sciences of Anhui Medical University, No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Ziyue Zhao
- Department of Immunology, School of Basic Medical Sciences of Anhui Medical University, No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Ashley Arnold
- International College of Anhui Medical University, No. 81 Meishan road, Hefei, 230032, Anhui, China
| | - Qinglian Xu
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.
| | - Jiegou Xu
- Department of Immunology, School of Basic Medical Sciences of Anhui Medical University, No. 81 Meishan Road, Hefei, 230032, Anhui, China.
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12
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Chen W, Yan X, Tian T, Yan R, Wang X, Yu Z, Li Y, Zhang L, Han S. Integrated analysis of a lncRNA‑mRNA network reveals a potential mechanism underlying necrotizing enterocolitis. Mol Med Rep 2020; 22:423-435. [PMID: 32319640 PMCID: PMC7248486 DOI: 10.3892/mmr.2020.11083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 03/25/2020] [Indexed: 02/02/2023] Open
Abstract
Previous studies have shown that long non-coding RNAs (lncRNAs) serve important roles in necrotizing enterocolitis (NEC). However, the underlying mechanisms remain largely unknown. In order to examine the potential role of lncRNAs in NEC, the present study investigated lncRNA and mRNA expression profiles in NEC lesions and adjacent intestinal tissues using Next Generation Sequencing. A total of 4,202 differentially expressed lncRNAs (fold-change >2; P<0.05) and 7,860 differentially expressed mRNAs (fold-change >2; P<0.05) were identified. Moreover, 5 dysregulated lncRNAs and 5 mRNAs were randomly selected, and further assessed by reverse transcription-quantitative PCR in vitro. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses demonstrated that the differentially expressed lncRNAs were closely associated with NEC, and were enriched in ‘inflammatory response’, ‘Toll-like receptor binding’, ‘PPAR signaling pathway’, ‘PI3K-Akt signaling pathway’, ‘transforming growth factor-β signaling pathway’ and ‘hypoxia-inducible factor 1 signaling pathway’. In addition, co-expression analysis demonstrated that these lncRNAs, including lncRNA ENST00000623580, lncRNA NONHSAT180418.1, lncRNA NONHSAT125636.2 and NONHSAT087855.2, may mediate the pathogenesis and development of NEC via lncRNA-mRNA network interactions. Therefore, the present study provided a novel insight into the role of lncRNAs in NEC.
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Affiliation(s)
- Wenjuan Chen
- Department of Neonatology, Wuxi Children's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Xiangyun Yan
- Department of Neonatology, Wuxi Children's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Tian Tian
- Department of Neonatology, Wuxi Children's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Ru Yan
- Department of Neonatology, Wuxi Children's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Xingyun Wang
- Department of Neonatology, Wuxi Children's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Zhangbin Yu
- Department of Neonatology, Wuxi Children's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Yingzheng Li
- Department of Neonatology, Wuxi Children's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Le Zhang
- Department of Neonatology, Wuxi Children's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Shuping Han
- Department of Neonatology, Wuxi Children's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
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13
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Verma Y, Yadav A, Katara P. Mining of cancer core-genes and their protein interactome using expression profiling based PPI network approach. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2019.100583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Bai J, Zhang X, Kang X, Jin L, Wang P, Wang Z. Screening of core genes and pathways in breast cancer development via comprehensive analysis of multi gene expression datasets. Oncol Lett 2019; 18:5821-5830. [PMID: 31788055 PMCID: PMC6865771 DOI: 10.3892/ol.2019.10979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/13/2019] [Indexed: 01/16/2023] Open
Abstract
Breast cancer has been the leading cause of cancer-associated mortality in women worldwide. Perturbation of oncogene and tumor suppressor gene expression is generally considered as the fundamental cause of cancer initiation and progression. In the present study, three gene expression datasets containing information of breast cancer and adjacent normal tissues that were detected using traditional gene microarrays were downloaded and batch effects were removed with R programming software. The differentially expressed genes between breast cancer and normal tissue groups were closely associated with cancer development pathways. Interestingly, five pathways, including ‘extracellular matrix-receptor interaction’, ‘peroxisome proliferator-activated receptors signaling pathway’, ‘propanoate metabolism’, ‘pyruvate metabolism’ and ‘regulation of lipolysis in adipocytes’, were thoroughly connected by 10 genes. Patients with upregulation of six of these hub genes (acetyl-CoA carboxylase β, acyl-CoA dehydrogenase medium chain, adiponectin, C1Q and collagen domain containing, acyl-CoA synthetase short chain family member 2, phosphoenolpyruvate carboxykinase 1 and perilipin 1) exhibited improved breast cancer prognosis. Additionally, breast cancer-specific network analysis identified several gene-gene interaction modules. These gene clusters had strong interactions according to the scoring in the whole network, which may be important to the development of breast cancer. In conclusion, the present study may improve the understanding of the mechanisms of breast cancer and provide several valuable prognosis and treatment signatures.
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Affiliation(s)
- Jie Bai
- Department of Thyroid and Breast III, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
| | - Xiaoyu Zhang
- Department of Thyroid and Breast III, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
| | - Xiaoning Kang
- Department of Ultrasound II, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
| | - Lijun Jin
- Department of Thyroid and Breast III, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
| | - Peng Wang
- Department of Thyroid and Breast III, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
| | - Zunyi Wang
- Department of Thyroid and Breast III, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
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15
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Chen G, Li Y, Su Y, Zhou L, Zhang H, Shen Q, Du C, Li H, Wen Z, Xia Y, Tang W. Identification of candidate genes for necrotizing enterocolitis based on microarray data. Gene 2018; 661:152-159. [PMID: 29605607 DOI: 10.1016/j.gene.2018.03.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/21/2018] [Accepted: 03/28/2018] [Indexed: 11/15/2022]
Abstract
Necrotizing enterocolitis (NEC) is one of the most serious diseases that could threaten the life of neonates. However the current opinions about the pathogenesis or how to prevent or treat the disease are still ambiguous. The purpose of the present study was to identify the key genes of this disease and provide new insights into the mechanism of NEC. The gene expression data of GSE46619, including 5 specimens from NEC patients and 4 samples from surgical-control infants, were collected from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were screened with regard to NEC versus surgical-control group using Limma package in R software and Gene Ontology (GO) enrichment analysis and pathway enrichment analysis were conducted by means of Database for Annotation, Visualization and Integrated Discovery (DAVID) website subsequently. Furthermore the protein-protein interaction (PPI) network for DEGs was constructed using Cytoscape software and the most highly connected module was extracted using MCODE plugin from the PPI network. Moreover, the significantly enriched sub-pathways were identified using iSubpathwayMiner package in R software. A total of 2629 DEGs were screened out between NEC and control samples, including 367 up-regulated genes and 2262 down-regulated genes and they involved in different GO terms and pathways which may be associated with NEC onset and progression. PPI network and module analysis revealed that several genes were defined as hub genes including AGT, IL8 and KNG1. The sub-pathway analysis screened out 189 significantly enriched sub-pathways, including Tryptophan metabolism, Fatty acid metabolism, and Arachidonic acid metabolism. Genes in the corresponding sub-pathway, such as ACACB and CAT were regarded as critical genes in NEC. QRT-PCR was also conducted to identify the expression of the five key genes (AGT, IL8, KNG1, ACACB and CAT) in NEC samples. These findings have identified several hub genes (e.g., AGT, IL8, KNG1, ACACB and CAT) which were presumed to serve critical roles in NEC.
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Affiliation(s)
- Guanglin Chen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Yang Li
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Yang Su
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Lingling Zhou
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Hua Zhang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Qiyang Shen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Chunxia Du
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Hongxing Li
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Zechao Wen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Modern Toxicology (Nanjing Medical University), Ministry of Education, China
| | - Weibing Tang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China.
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16
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Schiavone S, Camerino GM, Mhillaj E, Zotti M, Colaianna M, De Giorgi A, Trotta A, Cantatore FP, Conte E, Bove M, Tucci P, Morgese MG, Trabace L. Visceral Fat Dysfunctions in the Rat Social Isolation Model of Psychosis. Front Pharmacol 2017; 8:787. [PMID: 29167640 PMCID: PMC5682313 DOI: 10.3389/fphar.2017.00787] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/17/2017] [Indexed: 01/18/2023] Open
Abstract
Medication with neuroleptics has been associated with adipose tissue dysfunctions and, in particular, with increased visceral fat amount. However, several studies suggested that antipsychotic treatment might not be the main responsible of fat mass accumulation, as this has been also described in not treated psychotic patients. One of the most used “drug-free” rodent models of psychosis is the social isolation rearing of young adult rats, which provides a non-pharmacologic method of inducing long-term alterations reminiscent of symptoms seen in psychotic patients. Recent data highlighted a crucial role of redox imbalance in adipose tissue dysfunctions, in terms of decreased antioxidant defense and increased reactive oxygen species (ROS). Here, we investigated possible oxidative stress-related biomolecular alterations associated with visceral fat increase in 7 week isolated rats. To this purpose, we quantified total and visceral fat amount by using dual-energy X-ray (DEXA) absorptiometry. On visceral fat, we analyzed the expression of specific ROS-producer genes (Nox1, Nox4, Hmox-1), antioxidant enzymes (Prdx1 and Ucp-1) and oxidative stress-induced damage markers (Cidea, Slc2a4, and Acacb). The impact of oxidative stress on beta3-adrenergic receptors (Adrb3), at both mRNA and protein level, was also assessed. We found that 7 weeks of social isolation induced an increase in total and visceral fat, associated with a decrease in Prdx1 (mRNA and protein) as well as Ucp-1 mRNA levels and an enhanced expression of Nox1 (mRNA and protein) and Hmox-1 mRNA. No differences were detected in Nox4 mRNA levels between grouped and isolated animals. Elevations in Cidea, Slc2a4, and Acacb expression in visceral fat of isolated animals accounted for oxidative stress-related damage in this tissue, further associated with a significant increase in Adrb3 mRNA and protein. Our results provide a novel understanding of the pathological link existing among psychosocial stress-induced psychosis, adipose tissue dysfunctions and redox imbalance, opening new therapeutic perspectives for the treatment of alterations in peripheral tissues associated with this mental disorder.
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Affiliation(s)
- Stefania Schiavone
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Giulia M Camerino
- Department of Pharmacy and Drug Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Emanuela Mhillaj
- Department of Physiology and Pharmacology, Sapienza Università di Roma, Rome, Italy
| | - Margherita Zotti
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Marilena Colaianna
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Angelo De Giorgi
- Dual Diagnosis Unit, Azienda Sanitaria Locale della Provincia di Foggia, Foggia, Italy
| | - Antonello Trotta
- Rheumatology Unit, Foggia City Hospital "Ospedali Riuniti", Foggia, Italy
| | | | - Elena Conte
- Department of Pharmacy and Drug Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Maria Bove
- Department of Physiology and Pharmacology, Sapienza Università di Roma, Rome, Italy
| | - Paolo Tucci
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Maria G Morgese
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Luigia Trabace
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
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17
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Hoebel AK, Drichel D, van de Vorst M, Böhmer AC, Sivalingam S, Ishorst N, Klamt J, Gölz L, Alblas M, Maaser A, Keppler K, Zink AM, Dixon MJ, Dixon J, Hemprich A, Kruse T, Graf I, Dunsche A, Schmidt G, Daratsianos N, Nowak S, Aldhorae KA, Nöthen MM, Knapp M, Thiele H, Gilissen C, Reutter H, Hoischen A, Mangold E, Ludwig KU. Candidate Genes for Nonsyndromic Cleft Palate Detected by Exome Sequencing. J Dent Res 2017; 96:1314-1321. [PMID: 28767323 DOI: 10.1177/0022034517722761] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nonsyndromic cleft palate only (nsCPO) is a facial malformation that has a livebirth prevalence of 1 in 2,500. Research suggests that the etiology of nsCPO is multifactorial, with a clear genetic component. To date, genome-wide association studies have identified only 1 conclusive common variant for nsCPO, that is, a missense variant in the gene grainyhead-like-3 ( GRHL3). Thus, the underlying genetic causes of nsCPO remain largely unknown. The present study aimed at identifying rare variants that might contribute to nsCPO risk, via whole-exome sequencing (WES), in multiply affected Central European nsCPO pedigrees. WES was performed in 2 affected first-degree relatives from each family. Variants shared between both individuals were analyzed for their potential deleterious nature and a low frequency in the general population. Genes carrying promising variants were annotated for 1) reported associations with facial development, 2) multiple occurrence of variants, and 3) expression in mouse embryonic palatal shelves. This strategy resulted in the identification of a set of 26 candidate genes that were resequenced in 132 independent nsCPO cases and 623 independent controls of 2 different ethnicities, using molecular inversion probes. No rare loss-of-function mutation was identified in either WES or resequencing step. However, we identified 2 or more missense variants predicted to be deleterious in each of 3 genes ( ACACB, PTPRS, MIB1) in individuals from independent families. In addition, the analyses identified a novel variant in GRHL3 in 1 patient and a variant in CREBBP in 2 siblings. Both genes underlie different syndromic forms of CPO. A plausible hypothesis is that the apparently nonsyndromic clefts in these 3 patients might represent hypomorphic forms of the respective syndromes. In summary, the present study identified rare variants that might contribute to nsCPO risk and suggests candidate genes for further investigation.
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Affiliation(s)
- A K Hoebel
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - D Drichel
- 3 German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,4 Cologne Center for Genomics, Department of Statistical Genetics and Bioinformatics, University of Cologne, Cologne, Germany
| | - M van de Vorst
- 5 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A C Böhmer
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - S Sivalingam
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - N Ishorst
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - J Klamt
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - L Gölz
- 6 Department of Orthodontics, University of Bonn, Bonn, Germany
| | - M Alblas
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - A Maaser
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - K Keppler
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - A M Zink
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - M J Dixon
- 7 Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - J Dixon
- 7 Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - A Hemprich
- 8 Department of Oral and Maxillo-Facial Surgery, University of Leipzig, Leipzig, Germany
| | - T Kruse
- 9 Department of Orthodontics, University of Cologne, Cologne, Germany
| | - I Graf
- 9 Department of Orthodontics, University of Cologne, Cologne, Germany
| | - A Dunsche
- 10 Clinics Karlsruhe, Department of Oral and Maxillo-Facial Surgery, Karlsruhe, Germany
| | - G Schmidt
- 11 Department of Cleft Lip and Cleft Palate Surgery, Humboldt University of Berlin, Berlin, Germany
| | - N Daratsianos
- 6 Department of Orthodontics, University of Bonn, Bonn, Germany
| | - S Nowak
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - K A Aldhorae
- 12 Department of Orthodontics, College of Dentistry, Dhamar University, Dhamar, Yemen
| | - M M Nöthen
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - M Knapp
- 13 Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - H Thiele
- 14 Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - C Gilissen
- 5 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - H Reutter
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,15 Department of Neonatology &Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - A Hoischen
- 5 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,16 Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,17 Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - E Mangold
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - K U Ludwig
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
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18
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Li L, Wang G, Li N, Yu H, Si J, Wang J. Identification of key genes and pathways associated with obesity in children. Exp Ther Med 2017; 14:1065-1073. [PMID: 28810559 PMCID: PMC5525596 DOI: 10.3892/etm.2017.4597] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 02/24/2017] [Indexed: 01/22/2023] Open
Abstract
The present study aimed to identify potential key genes and pathways in obese children in order to explore possible molecular mechanisms associated with child obesity. The array dataset GSE29718 was downloaded from the Gene Expression Omnibus database. Subcutaneous adipose tissue samples derived from 7 obese children and 8 lean children were selected for the analysis. Differentially expressed genes (DEGs) in samples from obese children compared with those from lean children were analyzed by the limma package. Gene ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes and Reactome pathway enrichment analyses for up and downregulated genes were performed. A protein-protein interaction (PPI) network was constructed with Cytoscape software and important genes associated with obesity were determined using IRegulon. A total of 199 DEGs (79 up and 120 downregulated genes) were identified in the samples of obese children compared with those from lean children. The PPI network was established with 103 nodes and 147 protein pairs. Matrix metalloproteinase 9 (MMP9) and acetyl-CoA carboxylase β (ACACB) were identified as hub genes in the PPI network and may therefore be marker genes for child obesity. In addition, upregulated DEGs were enriched in Reactome pathways associated with the immune system. Besides, MMP9 was upregulated in immune system processes as a GO term in the category Biological Processes. The results of the present study indicated that MMP9, ACACB and immune system pathways may have a significant role in child obesity.
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Affiliation(s)
- Ling Li
- Department of Paediatrics, Jinan Children's Hospital, Jinan, Shandong 250022, P.R. China
| | - Guangyu Wang
- Department of Paediatrics, Jinan Children's Hospital, Jinan, Shandong 250022, P.R. China
| | - Ning Li
- Department of Paediatrics, Jinan Children's Hospital, Jinan, Shandong 250022, P.R. China
| | - Haiyan Yu
- Department of Paediatrics, The Fifth People's Hospital of Jinan, Jinan, Shandong 250022, P.R. China
| | - Jianping Si
- Department of Pediatrics, The People's Hospital of Guangrao, Dongying, Shandong 257300, P.R. China
| | - Jiwen Wang
- Department of Neurology, Children's Medical Center, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China.,Brain Science Research Institute, Shandong University, Jinan, Shandong 250012, P.R. China.,Department of Neurology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200240, P.R. China
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19
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An L, Jiang H, Tang RN. TheACACBgene rs2268388 polymorphism is associated with nephropathy in Caucasian patients with diabetes: a meta-analysis. Ren Fail 2015; 37:925-8. [DOI: 10.3109/0886022x.2015.1052978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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20
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Li T, Shi Y, Yin J, Qin Q, Wei S, Nie S, Liu L. The association between lipid metabolism gene polymorphisms and nephropathy in type 2 diabetes: a meta-analysis. Int Urol Nephrol 2014; 47:117-30. [DOI: 10.1007/s11255-014-0843-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/10/2014] [Indexed: 12/15/2022]
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21
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Suburu J, Gu Z, Chen H, Chen W, Zhang H, Chen YQ. Fatty acid metabolism: Implications for diet, genetic variation, and disease. FOOD BIOSCI 2013; 4:1-12. [PMID: 24511462 DOI: 10.1016/j.fbio.2013.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cultures across the globe, especially Western societies, are burdened by chronic diseases such as obesity, metabolic syndrome, cardiovascular disease, and cancer. Several factors, including diet, genetics, and sedentary lifestyle, are suspected culprits to the development and progression of these health maladies. Fatty acids are primary constituents of cellular physiology. Humans can acquire fatty acids by de novo synthesis from carbohydrate or protein sources or by dietary consumption. Importantly, regulation of their metabolism is critical to sustain balanced homeostasis, and perturbations of such can lead to the development of disease. Here, we review de novo and dietary fatty acid metabolism and highlight recent advances in our understanding of the relationship between dietary influences and genetic variation in fatty acid metabolism and their role in chronic diseases.
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Affiliation(s)
- Janel Suburu
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Zhennan Gu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China ; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China ; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
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22
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Gaur U, Li K, Mei S, Liu G. Research progress in allele-specific expression and its regulatory mechanisms. J Appl Genet 2013; 54:271-83. [PMID: 23609142 DOI: 10.1007/s13353-013-0148-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/22/2013] [Accepted: 04/03/2013] [Indexed: 12/12/2022]
Abstract
Although the majority of genes are expressed equally from both alleles, some genes are differentially expressed. Organisms possess characteristics to preferentially express a particular allele under regulatory factors, which is termed allele-specific expression (ASE). It is one of the important genetic factors that lead to phenotypic variation and can be used to identify the variance of gene regulation factors. ASE indicates mechanisms such as DNA methylation, histone modifications, and non-coding RNAs function. Here, we review a broad survey of progress in ASE studies, and what this simple yet very effective approach can offer in functional genomics, and possible implications toward our better understanding of the underlying mechanisms of complex traits.
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Affiliation(s)
- Uma Gaur
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, People's Republic of China
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23
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Civelek M, Hagopian R, Pan C, Che N, Yang WP, Kayne PS, Saleem NK, Cederberg H, Kuusisto J, Gargalovic PS, Kirchgessner TG, Laakso M, Lusis AJ. Genetic regulation of human adipose microRNA expression and its consequences for metabolic traits. Hum Mol Genet 2013; 22:3023-37. [PMID: 23562819 DOI: 10.1093/hmg/ddt159] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The genetics of messenger RNA (mRNA) expression has been extensively studied in humans and other organisms, but little is known about genetic factors contributing to microRNA (miRNA) expression. We examined natural variation of miRNA expression in adipose tissue in a population of 200 men who have been carefully characterized for metabolic syndrome (MetSyn) phenotypes as part of the Metabolic Syndrome in Men (METSIM) study. We genotyped the subjects using high-density single-nucleotide polymorphism microarrays and quantified the mRNA abundance using genome-wide expression arrays and miRNA abundance using next-generation sequencing. We reliably quantified 356 miRNA species that were expressed in human adipose tissue, a limited number of which made up most of the expressed miRNAs. We mapped the miRNA abundance as an expression quantitative trait and determined cis regulation of expression for nine of the miRNAs and of the processing of one miRNA (miR-28). The degree of genetic variation of miRNA expression was substantially less than that of mRNAs. For the majority of the miRNAs, genetic regulation of expression was independent of the expression of mRNA from which the miRNA is transcribed. We also showed that for 108 miRNAs, mapped reads displayed widespread variation from the canonical sequence. We found a total of 24 miRNAs to be significantly associated with MetSyn traits. We suggest a regulatory role for miR-204-5p which was predicted to inhibit acetyl coenzyme A carboxylase β, a key fatty acid oxidation enzyme that has been shown to play a role in regulating body fat and insulin resistance in adipose tissue.
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Affiliation(s)
- Mete Civelek
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
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Ma L, Murea M, Snipes JA, Marinelarena A, Krüger J, Hicks PJ, Langberg KA, Bostrom MA, Cooke JN, Suzuki D, Babazono T, Uzu T, Tang SCW, Mondal AK, Sharma NK, Kobes S, Antinozzi PA, Davis M, Das SK, Rasouli N, Kern PA, Shores NJ, Rudel LL, Blüher M, Stumvoll M, Bowden DW, Maeda S, Parks JS, Kovacs P, Hanson RL, Baier LJ, Elbein SC, Freedman BI. An ACACB variant implicated in diabetic nephropathy associates with body mass index and gene expression in obese subjects. PLoS One 2013; 8:e56193. [PMID: 23460794 PMCID: PMC3584087 DOI: 10.1371/journal.pone.0056193] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 01/07/2013] [Indexed: 02/04/2023] Open
Abstract
Acetyl coenzyme A carboxylase B gene (ACACB) single nucleotide polymorphism (SNP) rs2268388 is reproducibly associated with type 2 diabetes (T2DM)-associated nephropathy (DN). ACACB knock-out mice are also protected from obesity. This study assessed relationships between rs2268388, body mass index (BMI) and gene expression in multiple populations, with and without T2DM. Among subjects without T2DM, rs2268388 DN risk allele (T) associated with higher BMI in Pima Indian children (n = 2021; p-additive = 0.029) and African Americans (AAs) (n = 177; p-additive = 0.05), with a trend in European Americans (EAs) (n = 512; p-additive = 0.09), but not Germans (n = 858; p-additive = 0.765). Association with BMI was seen in a meta-analysis including all non-T2DM subjects (n = 3568; p-additive = 0.02). Among subjects with T2DM, rs2268388 was not associated with BMI in Japanese (n = 2912) or EAs (n = 1149); however, the T allele associated with higher BMI in the subset with BMI≥30 kg/m(2) (n = 568 EAs; p-additive = 0.049, n = 196 Japanese; p-additive = 0.049). Association with BMI was strengthened in a T2DM meta-analysis that included an additional 756 AAs (p-additive = 0.080) and 48 Hong Kong Chinese (p-additive = 0.81) with BMI≥30 kg/m(2) (n = 1575; p-additive = 0.0033). The effect of rs2268388 on gene expression revealed that the T risk allele associated with higher ACACB messenger levels in adipose tissue (41 EAs and 20 AAs with BMI>30 kg/m(2); p-additive = 0.018) and ACACB protein levels in the liver tissue (mixed model p-additive = 0.03, in 25 EA bariatric surgery patients with BMI>30 kg/m(2) for 75 exams). The T allele also associated with higher hepatic triglyceride levels. These data support a role for ACACB in obesity and potential roles for altered lipid metabolism in susceptibility to DN.
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Affiliation(s)
- Lijun Ma
- Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America.
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25
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Fang X, Netzer M, Baumgartner C, Bai C, Wang X. Genetic network and gene set enrichment analysis to identify biomarkers related to cigarette smoking and lung cancer. Cancer Treat Rev 2012; 39:77-88. [PMID: 22789435 DOI: 10.1016/j.ctrv.2012.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/03/2012] [Accepted: 06/06/2012] [Indexed: 10/28/2022]
Abstract
OBJECTIVES Cigarette smoking is the most demonstrated risk factor for the development of lung cancer, while the related genetic mechanisms are still unclear. METHODS The preprocessed microarray expression dataset was downloaded from Gene Expression Omnibus database. Samples were classified according to the disease state, stage and smoking state. A new computational strategy was applied for the identification and biological interpretation of new candidate genes in lung cancer and smoking by coupling a network-based approach with gene set enrichment analysis. MEASUREMENTS Network analysis was performed by pair-wise comparison according to the disease states (tumor or normal), smoking states (current smokers or nonsmokers or former smokers), or the disease stage (stages I-IV). The most activated metabolic pathways were identified by gene set enrichment analysis. RESULTS Panels of top ranked gene candidates in smoking or cancer development were identified, including genes involved in cell proliferation and drug metabolism like cytochrome P450 and WW domain containing transcription regulator 1. Semaphorin 5A and protein phosphatase 1F are the common genes represented as major hubs in both the smoking and cancer related network. Six pathways, e.g. cell cycle, DNA replication, RNA transport, protein processing in endoplasmic reticulum, vascular smooth muscle contraction and endocytosis were commonly involved in smoking and lung cancer when comparing the top ten selected pathways. CONCLUSION New approach of bioinformatics for biomarker identification and validation can probe into deep genetic relationships between cigarette smoking and lung cancer. Our studies indicate that disease-specific network biomarkers, interaction between genes/proteins, or cross-talking of pathways provide more specific values for the development of precision therapies for lung.
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Affiliation(s)
- Xiaocong Fang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.
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