基于基因组规模代谢模型探究影响肝癌细胞生长的关键基因Investigation of key genes for hepatocellular carcinoma tumor cell growth based on genome-scale metabolic model
徐轶舟;王卓;
摘要(Abstract):
基于全基因组规模代谢模型的模拟分析已被成功应用于探索包括癌症在内的多种疾病的发生机制,通过模拟基因敲除对肿瘤细胞生长的影响,鉴别关键代谢重编程节点。通过分析肝细胞肝癌(Hepatocellular carcinoma, HCC)不同于正常肝细胞的代谢差异,发现AKG能够调节肿瘤生长,是潜在的抗癌药物靶点;而TECR在HCC细胞中的重要性降低使其成为潜在的抗肿瘤位点。HCC肝癌细胞在胆固醇合成通路上存在代谢重编程:DHCR24和HMGCS2基因的缺失可以帮助肿瘤细胞避免正常凋亡,而IDI2基因的存在能够增强肿瘤细胞增殖、迁移能力;胆碱代谢物可以影响脂肪酸合成通路从而促进炎症反应来加速癌症发展的进程。
关键词(KeyWords): 全基因组规模代谢模型;肝细胞肝癌;基因敲除;胆固醇合成;L-氯化棕榈酰肉碱
基金项目(Foundation): 国家重点研发计划(2017YFC0908105);; 国家自然科学基金面上项目(32070679)
作者(Author): 徐轶舟;王卓;
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DOI:
参考文献(References):
- [1]FERLAY J,SOERJOMATARAM I,DIKSHIT R,et al.Cancer incidence and mortality worldwide:sources,methods and major patterns in GLOBOCAN 2012 [J].International Journal of Cancer,2015,136(5):359-386.
- [2]WARD P S,THOMPSON C B.Metabolic reprogramming:a cancer hallmark even warburg did not anticipate [J].Cancer Cell,2012,21(3):297-308.
- [3]THIELE I,SWAINSTON N,FLEMING R M,et al.A community-driven global reconstruction of human metabolism [J].Nature Biotechnology,2013,31(5):419-425.
- [4]AGREN R,BORDEL S,MARDINOGLU A,et al.Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT [J].PLoS Computational Biology,2012,8(5):e1002518.
- [5]MARDINOGLU A,NIELSEN J.New paradigms for metabolic modeling of human cells [J].Current Opinion in Biotechnology,2015,34:91-97.
- [6]UHLEN M,ZHANG C,LEE S,et al.A pathology atlas of the human cancer transcriptome [J].Science (New York,NY),2017,357(6352):eaan2507.
- [7]UHLEN M,FAGERBERG L,HALLSTROM B M,et al.Proteomics.Tissue-based map of the human proteome [J].Science (New York,NY),2015,347(6220):1260419.
- [8]GATTO F,NOOKAEW I,NIELSEN J.Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma [J].Proceedings of the National Academy of Sciences of the United States of America,2014,111(9):866-875.
- [9]MARDINOGLU A,AGREN R,KAMPF C,et al.Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease [J].Nature Communications,2014,5(3083):3083.
- [10]ORTH J D,THIELE I,PALSSON B O.What is flux balance analysis?[J].Nature Biotechnology,2010,28(3):245-248.
- [11]HEIRENDT L,ARRECKX S,PFAU T,et al.Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 [J].Nature Protocols,2019,14(3):639-702.
- [12]WANG H,MARCISAUSKAS S,SANCHEZ B J,et al.RAVEN 2.0:a versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor [J].PLoS Computational Biology,2018,14(10):e1006541.
- [13]BEKTAS M,PAYNE S G,LIU H,et al.A novel acylglycerol kinase that produces lysophosphatidic acid modulates cross talk with EGFR in prostate cancer cells [J].The Journal of Cell Biology,2005,169(5):801-811.
- [14]KHAN N,SHAH P P,BAN D,et al.Solution structure and functional investigation of human guanylate kinase reveals allosteric networking and a crucial role for the enzyme in cancer [J].The Journal of Biological Chemistry,2019,294(31):11920-11933.
- [15]GLUNDE K,PENET M F,JIANG L,et al.Choline metabolism-based molecular diagnosis of cancer:an update [J].Expert Review of Molecular Diagnostics,2015,15(6):735-747.
- [16]IKAWA-YOSHIDA A,MATSUO S,KATO A,et al.Hepatocellular carcinoma in a mouse model fed a choline-deficient,L-amino acid-defined,high-fat diet [J].International Journal of Experimental Pathology,2017,98(4):221-233.
- [17]WANG Y H,LIU C L,CHIU W C,et al.HMGCS2 mediates ketone production and regulates the proliferation and metastasis of hepatocellular carcinoma [J].Cancers,2019,11(12):1876.
- [18]WU C,MILOSLAVSKAYA I,DEMONTIS S,et al.Regulation of cellular response to oncogenic and oxidative stress by Seladin-1 [J].Nature,2004,432(7017):640-645.
- [19]KUHAJDA F P,JENNER K,WOOD F D,et al.Fatty acid synthesis:a potential selective target for antineoplastic therapy [J].Proceedings of the National Academy of Sciences of the United States of America,1994,91(14):6379-6383.
- [20]GOBIN S,THUILLIER L,JOGL G,et al.Functional and structural basis of carnitine palmitoyltransferase 1A deficiency [J].The Journal of Biological Chemistry,2003,278(50):50428-50434.
- [21]AL-BAKHEIT A,TRAKA M,SAHA S,et al.Accumulation of palmitoylcarnitine and its effect on pro-inflammatory pathways and calcium influx in prostate cancer [J].The Prostate,2016,76(14):1326-1337.
- [22]WETTERSTEN H I,HAKIMI A A,MORIN D,et al.Grade-dependent metabolic reprogramming in kidney cancer revealed by combined proteomics and metabolomics analysis [J].Cancer Research,2015,75(12):2541-2552.
- [23]YALIGAR J,TEOH W W,OTHMAN R,et al.Longitudinal metabolic imaging of hepatocellular carcinoma in transgenic mouse models identifies acylcarnitine as a potential biomarker for early detection [J].Scientific Reports,2016,6:20299.
- [24]ZERENTURK E J,SHARPE L J,IKONEN E,et al.Desmosterol and DHCR24:unexpected new directions for a terminal step in cholesterol synthesis [J].Progress in Lipid Research,2013,52(4):666-680.
- [25]TABAS I,FEINMARK S J,BEATINI N.The reactivity of desmosterol and other shellfish- and xanthomatosis-associated sterols in the macrophage sterol esterification reaction [J].The Journal of Clinical Investigation,1989,84(6):1713-1721.