Identification of key target genes and pathway analysis in nonalcoholic fatty liver disease via integrated bioinformatics analysis
References
- Erman H, Beydogan E, Cetin SI, Boyuk B. Endocan: A Biomarker for Hepatosteatosis in Patients with Metabolic Syndrome. Mediators Inflamm. 2020; 2020: 3534042.
- Aizawa M, Inagaki S, Moriyama M, Asano K, Kakehashi M. Modeling the natural history of fatty liver using lifestyle-related risk factors: Effects of body mass index (BMI) on the life-course of fatty liver. PLoS One. 2019; 14(10):e0223683.
- Zelber-Sagi S, Lotan R, Shlomai A, Webb M, Harrari G, Buch A, et al. Predictors for incidence and remission of NAFLD in the general population during a seven-year prospective follow-up. Journal of hepatology. 2012; 56(5): 1145-1151.
- Sookoian S, Pirola CJ. Review article: shared disease mechanisms between non-alcoholic fatty liver disease and metabolic syndrome - translating knowledge from systems biology to the bedside. Aliment Pharmacol Ther. 2019; 49(5): 516-527.
- Friedman SL, Neuschwander-Tetri BA, Rinella M, Sanyal AJ. Mechanisms of NAFLD development and therapeutic strategies. Nat Med. 2018; 24(7):908-922.
- Rinella ME. Nonalcoholic fatty liver disease: a systematic review. JAMA. 2015; 313(22):2263-73.
- Noureddin M, Rinella ME. Nonalcoholic Fatty liver disease, diabetes, obesity, and hepatocellular carcinoma. Clin Liver Dis. 2015; 19(2):361-79.
- Fabbrini E, Magkos F, Mohammed BS, Pietka T, Abumrad NA, Patterson BW, et al. Intrahepatic fat, not visceral fat, is linked with metabolic complications of obesity. Proc Natl Acad Sci USA. 2009;106(36):15430-5.
- Konerman MA, Jones JC, Harrison SA. Pharmacotherapy for NASH: Current and emerging. J Hepatol. 2018; 68(2):362-375.
- Sookoian S, Rosselli MS, Gemma C, Burgueño AL, Fernández Gianotti T, Castaño GO, Pirola CJ. Epigenetic regulation of insulin resistance in nonalcoholic fatty liver disease: impact of liver methylation of the peroxisome proliferator-activated receptor γ coactivator 1α promoter. Hepatology. 2010; 52(6):1992-2000
- Liu NK, Xu XM. MicroRNA in central nervous system trauma and degenerative disorders. Physiol Genomics. 2011; 43(10):571-80
- Piazzolla VA, Mangia A. Noninvasive Diagnosis of NAFLD and NASH. Cells. 2020; 9(4):1005
- Zou B, Yeo YH, Nguyen VH, Cheung R, Ingelsson E, Nguyen MH. Prevalence, characteristics and mortality outcomes of obese, nonobese and lean NAFLD in the United States, 1999-2016. J Intern Med. 2020; 288(1):139-151
- Lefebvre P, Lalloyer F, Baugé E, Pawlak M, Gheeraert C, Dehondt H, et al. Interspecies NASH disease activity whole-genome profiling identifies a fibrogenic role of PPARα-regulated dermatopontin. JCI Insight. 2017 Jul 6;2(13):e92264
- Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, et al. NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res. 2007; 35(Database issue):D760-5
- Braschi B, Denny P, Gray K, Jones T, Seal R, Tweedie S, et al. Genenames.org: the HGNC and VGNC resources in 2019. Nucleic Acids Res. 2019; 47(D1):D786-D792
- Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015; 43 (7):e47
- Wang L, Cao C, Ma Q, Zeng Q, Wang H, Cheng Z, et al. RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications. BMC Plant Biol. 2014; 14:169
- Bonow RO. Braunwald` s Heart Disease: A Textbook of Cardiovascular Medicine, Single Volume, 9th Edition.
- Szekely, G., Rizzo, M. Hierarchical Clustering via Joint Between-Within Distances: Extending Ward’s Minimum Variance Method. Journal of Classification; 2005; 22, 151–183
- Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57
- Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009; 37(1):1-13
- Huang Z, Shi J, Gao Y, Cui C, Zhang S, Li J, et al. HMDD v3.0: a database for experimentally supported human microRNA-disease associations. Nucleic Acids Res. 2019; 47(D1):D1013-D1017
- Paraskevopoulou MD, Vlachos IS, Karagkouni D, Georgakilas G, Kanellos I, Vergoulis T, et al. DI-ANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res. 2016; 44(D1):D231-8
- Li JH, Liu S, Zhou H, Qu LH, Yang JH. StarBase v2.0: Decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014; 42(Database issue):D92-7
- Thorn CF, Klein TE, Altman RB. PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Methods Mol Biol. 2005; 311:179-91
- Chen HJ, Liu J. Actein ameliorates hepatic steatosis and fibrosis in high fat diet-induced NAFLD by regulation of insulin and leptin resistant. Biomed Pharmacother. 2018; 97: 1386-1396.
- Pan X, Zheng M, Zou T, Liu W, Gu X, Zhang X, et al. The LEPR K109R and Q223R Might Contribute to the Risk of NAFLD: A Meta-Analysis. Curr Mol Med. 2018; 18(2): 91-99.
- Zhang Y, Xiang D, Hu X, Ruan Q, Wang L, Bao Z. Identification and study of differentially expressed miRNAs in aged NAFLD rats based on high-throughput sequencing. Ann Hepatol. 2020; 19(3):302-312
- Romeo S, Kozlitina J, Xing C, Pertsemlidis A, Cox D, Pennacchio LA, et al. Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. 2008; 40(12): 1461-1465.
- Kozlitina J, Smagris E, Stender S, Nordestgaard BG, Cohen JCJNG. Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease. 2014; 46(4): 352-356.
- Mancina RM, Dongiovanni P, Petta S, Pingitore P, Meroni M, Rametta R, et al. The MBOAT7-TMC4 Variant rs641738 Increases Risk of Nonalcoholic Fatty Liver Disease in Individuals of European Descent. 2016; 150(5): 1219-1230.e1216.
- Eslam M, Hashem AM, Leung R, Romero-Gomez M, Berg T, Dore GJ, et al. ; International Hepatitis C Genetics Consortium (IHCGC). Interferon-λ rs12979860 genotype and liver fibrosis in viral and non-viral chronic liver disease. Nat Commun. 2015; 6:6422.
- Petta S, Valenti L, Marra F, Grimaudo S, Tripodo C, Bugianesi E, et al. MERTK rs4374383 polymorphism affects the severity of fibrosis in non-alcoholic fatty liver disease. 2016; 64(3): 682-690.
- Aller R, De Luis DA, Izaola O, González Sagrado M, Conde R, Pacheco D, et al. Lys656Asn polymorphism of leptin receptor, leptin levels and insulin resistance in patients with non alcoholic fatty liver disease. Eur Rev Med Pharmacol Sci. 2012;16(3):335-41.
- An BQ, Lu LL, Yuan C, Xin YN, Xuan SY. Leptin Receptor Gene Polymorphisms and the Risk of Non-Alcoholic Fatty Liver Disease and Coronary Atherosclerosis in the Chinese Han Population. Hepat Mon. 2016; 16(4):e35055.
- Neville LF, Mathiak G, Bagasra O. The immunobiology of interferon-gamma inducible protein 10 kD (IP-10): a novel, pleiotropic member of the C-X-C chemokine superfamily. Cytokine Growth Factor Rev. 1997; 8(3):207-19.
- Luster AD, Unkeless JC, Ravetch JV. Gamma-interferon transcriptionally regulates an early-response gene containing homology to platelet proteins. Nature. 1985; 315(6021):672-6.
- Bertola A, Bonnafous S, Anty R, Patouraux S, Saint-Paul MC, Iannelli A, et al. Hepatic expression patterns of inflammatory and immune response genes associated with obesity and NASH in morbidly obese patients. PLoS One. 2010; 5(10):e13577.
- Zhang X, Shen J, Man K, Chu ES, Yau TO, Sung JC, et al. CXCL10 plays a key role as an inflammatory mediator and a non-invasive biomarker of non-alcoholic steatohepatitis. Journal of hepatology. 2014; 61(6): 1365-1375.
- Dong XC, Copps KD, Guo S, Li Y, Kollipara R, Depinho RA, et al. Inactivation of Hepatic Foxo1 by Insulin Signaling Is Required for Adaptive Nutrient Homeostasis and Endocrine Growth Regulation. 2008; 8(1): 0-76.
- Munekata K, Sakamoto K. Forkhead transcription factor Foxo1 is essential for adipocyte differentiation. In Vitro Cell Dev Biol Anim. 2009; 45(10):642-51.
- Li Y, Ma Z, Jiang S, Hu W, Li T, Di S, et al. A global perspective on FOXO1 in lipid metabolism and lipid-related diseases. Prog Lipid Res. 2017; 66: 42-49.
- Xin Z, Ma Z, Hu W, Jiang S, Yang Z, Li T, et al. FOXO1/3: Potential suppressors of fibrosis. Ageing Res Rev. 2018; 41: 42-52.
- Valenti L, Dongiovanni P, Rametta R, Fracanzani AL, Fargion SJD, Disease L. FOXO1 genotype influences the susceptibility to and severity of NAFLD by modulating FOXO1 expression. 2009; 41(3):A2–A3.
DOI: https://doi.org/10.2478/bjmg-2022-0006 | Journal eISSN: 2199-5761
Language: English
Page range: 25 - 34
Published on: Mar 1, 2023
Published by: Macedonian Academy of Sciences and Arts
In partnership with: Paradigm Publishing Services
Publication frequency: 2 issues per year
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© 2023 X. Chen, L. Zhang, Y. Wang, R. Li, M. Yang, L. Gao, published by Macedonian Academy of Sciences and Arts
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.