Biomarkers of Cholestasis

References

• Pollock G , MinukGY. Diagnostic considerations for cholestatic liver disease. J. Gastroenterol. Hepatol.32(7), 1303–1309 (2017).
   PubMed Web of Science ®Google Scholar
• Jüngst C , LammertF. Cholestatic liver disease. Dig. Dis.31(1), 152–154 (2013).
   PubMed Web of Science ®Google Scholar
• Lu LG , ChenCW, ChengJet al. Consensus on the diagnosis and treatment of cholestatic liver diseases (2015, China). J. Dig. Dis.17(3), 137–154 (2016).
   PubMed Web of Science ®Google Scholar
• EASL . European Association for the Study of the Liver Clinical Practice Guidelines: management of cholestatic liver diseases. J. Hepatol.51(2), 237–267 (2009).
   PubMed Web of Science ®Google Scholar
• Nguyen KD , SundaramV, AyoubWS. Atypical causes of cholestasis. World J. Gastroenterol.20(28), 9418–9426 (2014).
   PubMed Web of Science ®Google Scholar
• Cao X , GaoY, ZhangWet al. Cholestasis morbidity rate in first-hospitalized patients with chronic liver disease in Shanghai. Chinese J. Hepatol.23(8), 569–573 (2015).
   PubMedGoogle Scholar
• Onofrio FQ , HirschfieldGM. The pathophysiology of cholestasis and its relevance to clinical practice. Clin. Liver Dis.15(3), 110–114 (2020).
   Google Scholar
• Marrer E , DieterleF. Impact of biomarker development on drug safety assessment. Toxicol. Appl. Pharmacol.243(2), 167–179 (2010).
   PubMed Web of Science ®Google Scholar
• Hardy T , MannDA. Epigenetics in liver disease: from biology to therapeutics. Gut.65(11), 1895–1905 (2016).
   PubMed Web of Science ®Google Scholar
• Strimbu K , TavelJA. What are biomarkers?Curr. Opin. HIV AIDS.5(6), 463–466 (2010).
   PubMed Web of Science ®Google Scholar
• Babrak LM , MenetskiJ, RebhanMet al. Traditional and digital biomarkers: two worlds apart? Digit Biomarkers 3(2), 92–102 (2019).
   PubMedGoogle Scholar
• Levy C , LindorKD. Management of osteoporosis, fat-soluble vitamin deficiencies, and hyperlipidemia in primary biliary cirrhosis. Clin. Liver Dis.7(4), 901–910 (2003).
   PubMedGoogle Scholar
• Phillips JR , AnguloP, PettersonT, LindorKD. Fat-soluble vitamin levels in patients with primary biliary cirrhosis. Am. J. Gastroenterol.96(9), 2745–2750 (2001).
   PubMed Web of Science ®Google Scholar
• Rogoveanu I , GheoneaDI, SaftoiuA, CiureaT. The role of imaging methods in identifying the causes of extrahepatic cholestasis. J. Gastrointest. Liver Dis.15(3), 265–271 (2006).
   PubMedGoogle Scholar
• Cieszanowski A , ChomickaD, AndrzejewskaM, PruszyńskiB, PawlakJ, MustafaAM. Imaging techniques in patients with biliary obstruction. Med. Sci. Monit.6(6), 1197–1202 (2000).
   PubMedGoogle Scholar
• Corpechot C . Utility of noninvasive markers of fibrosis in cholestatic liver diseases. Clin. Liver Dis.20(1), 143–158 (2016).
   PubMed Web of Science ®Google Scholar
• Patel K , SebastianiG. Limitations of noninvasive tests for assessment of liver fibrosis. JHEP Reports Innov. Hepatol.2(2), 100067 (2020).
   PubMedGoogle Scholar
• Toosi AEK . Liver fibrosis: causes and methods of assessment, a review. Rom. J. Intern. Med.53(4), 304–314 (2015).
   PubMedGoogle Scholar
• Frulio N , TrillaudH. Ultrasound elastography in liver. Diagn. Interv. Imaging94(5), 515–534 (2013).
   PubMedGoogle Scholar
• Ramaiah SK . A toxicologist guide to the diagnostic interpretation of hepatic biochemical parameters. Food Chem. Toxicol.45(9), 1551–1557 (2007).
   PubMed Web of Science ®Google Scholar
• Lindblom P , RafterI, CopleyCet al. Isoforms of alanine aminotransferases in human tissues and serum-differential tissue expression using novel antibodies. Arch. Biochem. Biophys.466(1), 66–77 (2007).
   PubMed Web of Science ®Google Scholar
• Yang RZ , BlaileanuG, HansenBC, ShuldinerAR, GongDW. cDNA cloning, genomic structure, chromosomal mapping, and functional expression of a novel human alanine aminotransferase. Genomics79(3), 445–450 (2002).
   PubMed Web of Science ®Google Scholar
• Sharma U , PalD, PrasadR. Alkaline phosphatase: an overview. Indian J. Clin. Biochem.29(3), 269–278 (2014).
   PubMedGoogle Scholar
• Accatino L , FigueroaC, PizarroM, SolísN. Enhanced biliary excretion of canalicular membrane enzymes in estrogen-induced and obstructive cholestasis, and effects of different bile acids in the isolated perfused rat liver. J. Hepatol.22(6), 658–670 (1995).
   PubMed Web of Science ®Google Scholar
• Deng JT , HoylaertsMF, DeBroe ME, Van HoofVO. Hydrolysis of membrane-bound liver alkaline phosphatase by GPI-PLD requires bile salts. Am. J. Physiol.271(4 Pt 1), G655–G663 (1996).
   PubMedGoogle Scholar
• Hatoff DE , HardisonWGM. Bile acid-dependent secretion of alkaline phosphatase in rat bile. Hepatology.2(4), 433–439 (1982).
   PubMed Web of Science ®Google Scholar
• Vinken M , MaesM, VanhaeckeT, RogiersV. Drug-induced liver injury: mechanisms, types and biomarkers. Curr. Med. Chem.20(24), 3011–3021 (2013).
   PubMed Web of Science ®Google Scholar
• Price CP . Multiple forms of human serum alkaline phosphatase: detection and quantitation. Ann. Clin. Biochem.30(4), 355–372 (1993).
   PubMed Web of Science ®Google Scholar
• Sotil EU , JensenDM. Serum enzymes associated with cholestasis. Clin. Liver Dis.8(1), 41–54 (2004).
   PubMedGoogle Scholar
• Hall P , CashJ. What is the real function of the Liver “Function” tests?Ulster Med. J.81(1), 30–36 (2012).
   PubMedGoogle Scholar
• Rej R , ShawLM. Measurement of aminotransferases: part 1. Aspartate aminotransferase. Crit. Rev. Clin. Lab. Sci.21(2), 99–186 (1984).
   PubMed Web of Science ®Google Scholar
• Boyde TRC , LatnerAL. Starch-gel electrophoresis of trans-aminases in human-tissue extracts and sera. Biochem. J.82, 51 (1962).
   Web of Science ®Google Scholar
• Reichling JJ , KaplanMM. Clinical use of serum enzymes in liver disease. Dig. Dis. Sci.33(12), 1601–1614 (1988).
   PubMed Web of Science ®Google Scholar
• Hanigan MH , FriersonHF. Immunohistochemical detection of γ-glutamyl transpeptidase in normal human tissue. J. Histochem. Cytochem.44(10), 1101–1108 (1996).
   PubMed Web of Science ®Google Scholar
• Grisk O , KüsterU, AnsorgeS. The activity of γ-glutamyl transpeptidase (γ-gt) in populations of mononuclear cells from human peripheral blood. Biol. Chem. Hoppe. Seyler.374(1–6), 287–290 (1993).
   PubMedGoogle Scholar
• Novogrodsky A , TateSS, MeisterA. γ Glutamyl transpeptidase, a lymphoid cell surface marker: relationship to blastogenesis, differentiation, and neoplasia. Proc. Natl Acad. Sci. USA73(7), 2414–2418 (1976).
   PubMed Web of Science ®Google Scholar
• Sheehan M , HaythornP. Predictive values of various liver function tests with respect to the diagnosis of liver disease. Clin. Biochem.12(6), 262–263 (1979).
   PubMed Web of Science ®Google Scholar
• Whitfield JB . Gamma glutamyl transferase. Crit. Rev. Clin. Lab. Sci.38(4), 263–355 (2001).
   PubMed Web of Science ®Google Scholar
• Dixon TF , PurdomM. Serum 5-nucleotidase. J. Clin. Pathol.7(4), 341–343 (1954).
   PubMed Web of Science ®Google Scholar
• Singh K . Evaluation and interpretation of biomarkers of liver diseases. Int. J. Res. Heal. Sci.1(3), 213–223 (2013).
   Google Scholar
• Smith GS , WalterGL, WalkerRM. Clinical Pathology in Non-Clinical Toxicology Testing (3rd Edition). Elsevier,CA, USA (2013).
   Google Scholar
• Shah R , JohnS. Cholestatic Jaundice (Cholestasis, Cholestatic Hepatitis).StatPearls Publishing, CA, USA (2020).
   Google Scholar
• Kamisawa T , NakazawaT, TazumaSet al. Clinical practice guidelines for IgG4-related sclerosing cholangitis. J. Hepatobiliary. Pancreat. Sci.26(1), 9–42 (2019).
   PubMed Web of Science ®Google Scholar
• Chatterjee S , AnnaertP. Drug-induced cholestasis: mechanisms, models, and markers. Curr. Drug Metab.19(10), 808–818 (2018).
   PubMed Web of Science ®Google Scholar
• Tan D , GoodmanZD. Liver biopsy in primary biliary cholangitis: indications and interpretation. Clin. Liver Dis.22(3), 579–588 (2018).
   PubMed Web of Science ®Google Scholar
• Lefkowitch JH . Histological assessment of cholestasis. Clin. Liver Dis.8(1), 27–40 (2004).
   PubMedGoogle Scholar
• Zen Y , HübscherSG, NakanumaY. Bile duct diseases. In: MacSween's Pathology of the Liver.Elsevier Inc., Oxford, UK, 515–593 (2018).
   Google Scholar
• Gasmi B , KleinerDE. Liver histology: diagnostic and prognostic features. Clin. Liver Dis.24(1), 61–74 (2020).
   PubMed Web of Science ®Google Scholar
• Rockey DC , CaldwellSH, GoodmanZD, NelsonRC, SmithAD. Liver biopsy. Hepatology49(3), 1017–1044 (2009).
   PubMed Web of Science ®Google Scholar
• Tapper EB , LokASF. Use of liver imaging and biopsy in clinical practice. N. Engl. J. Med.377(8), 756–768 (2017).
   PubMed Web of Science ®Google Scholar
• The French METAVIR Cooperative Study Group . Intraobserver and interobserver variations in liver biopsy interpretation in patients with chronic hepatitis C. Hepatology20(1 Pt 1), 15–20 (1994).
   PubMed Web of Science ®Google Scholar
• Jansen PLM , GhallabA, VartakNet al. The ascending pathophysiology of cholestatic liver disease. Hepatology65(2), 722–738 (2017).
   PubMed Web of Science ®Google Scholar
• Reichert MC , HallRA, KrawczykM, LammertF. Genetic determinants of cholangiopathies: molecular and systems genetics. Biochim. Biophys. Acta – Mol. Basis Dis.1864(4), 1484–1490 (2018).
   PubMed Web of Science ®Google Scholar
• Krawczyk M , MüllenbachR, WeberSN, ZimmerV, LammertF. Genome-wide association studies and genetic risk assessment of liver diseases. Nat. Rev. Gastroenterol. Hepatol.7(12), 669–681 (2010).
   PubMed Web of Science ®Google Scholar
• Cordell HJ . Detecting gene–gene interactions that underlie human diseases. Nat. Rev. Genet.10(6), 392–404 (2009).
   PubMed Web of Science ®Google Scholar
• Zondervan KT , CardonLR. The complex interplay among factors that influence allelic association. Nat. Rev. Genet.5(2), 89–100 (2004).
   PubMed Web of Science ®Google Scholar
• Buch S , SchafmayerC, VölzkeHet al. A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease. Nat. Genet.39(8), 995–999 (2007).
   PubMed Web of Science ®Google Scholar
• Katsika D , MagnussonP, KrawczykMet al. Gallstone disease in Swedish twins: risk is associated with ABCG8 D19H genotype. J. Intern. Med.268(3), 279–285 (2010).
   PubMed Web of Science ®Google Scholar
• Stokes CS , KrawczykM, LammertF. Gallstones: environment, lifestyle and genes. Dig. Dis.29(2), 191–201 (2011).
   PubMed Web of Science ®Google Scholar
• Joshita S , UmemuraT, TanakaE, OtaM. Genetics and epigenetics in the pathogenesis of primary biliary cholangitis. Clin. J. Gastroenterol.11(1), 11–18 (2018).
   PubMedGoogle Scholar
• Jiang X , KarlsenTH. Genetics of primary sclerosing cholangitis and pathophysiological implications. Nat. Rev. Gastroenterol. Hepatol.14(5), 279–295 (2017).
   PubMed Web of Science ®Google Scholar
• Karlsen TH , ChungBK. Genetic risk and the development of autoimmune liver disease. Dig. Dis.33(Suppl. 2), 13–24 (2015).
   PubMedGoogle Scholar
• Trivedi PJ , HirschfieldGM. The immunogenetics of autoimmune cholestasis. Clin. Liver Dis.20(1), 15–31 (2016).
   PubMed Web of Science ®Google Scholar
• Liu JZ , HovJR, FolseraasTet al. Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. Nat. Genet.45(6), 670–675 (2013).
   PubMed Web of Science ®Google Scholar
• Karlsen TH , LammertF, ThompsonRJ. Genetics of liver disease: from pathophysiology to clinical practice. J. Hepatol.62(Suppl. 1), S6–S14 (2015).
   PubMedGoogle Scholar
• Galoosian A , HanlonC, ZhangJ, HoltEW, YimamKK. Clinical updates in primary biliary cholangitis: trends, epidemiology, diagnostics, and new therapeutic approaches. J. Clin. Transl. Hepatol.8(1), 49–60 (2020).
   PubMed Web of Science ®Google Scholar
• Folseraas T , LiaskouE, AndersonCA, KarlsenTH. Genetics in PSC: what do the “risk genes” teach us?Clin. Rev. Allergy Immunol.48(2–3), 154–164 (2015).
   PubMed Web of Science ®Google Scholar
• Müllenbach R , LammertF. An update on genetic analysis of cholestatic liver diseases: digging deeper. Dig. Dis.29, 72–77 (2011).
   PubMed Web of Science ®Google Scholar
• Hirschfield GM , ChapmanRW, KarlsenTH, LammertF, LazaridisKN, MasonAL. The genetics of complex cholestatic disorders. Gastroenterology144(7), 1357–1374 (2013).
   PubMed Web of Science ®Google Scholar
• Waddington CH . The epigenotype 1942. Int. J. Epidemiol.41(1), 10–13 (2012).
   PubMed Web of Science ®Google Scholar
• Al Aboud NM , JialalI. Genetics, Epigenetic Mechanism. StatPearls Publishing, CA, USA. (2018).
   Google Scholar
• Li J , JinH, WangX. Epigenetic biomarkers: potential applications in gastrointestinal cancers. ISRN Gastroenterol.2014, 464015 (2014).
   PubMedGoogle Scholar
• Wang XW , HeegaardNHH, OrumH. MicroRNAs in liver disease. Gastroenterology142(7), 1431–1443 (2012).
   PubMed Web of Science ®Google Scholar
• García-Giménez JL , Seco-CerveraM, TollefsbolTOet al. Epigenetic biomarkers: current strategies and future challenges for their use in the clinical laboratory. Crit. Rev. Clin. Lab. Sci.54(7–8), 529–550 (2017).
   PubMed Web of Science ®Google Scholar
• Smith Z , RyersonD, KemperJK. Epigenomic regulation of bile acid metabolism: emerging role of transcriptional cofactors. Mol. Cell. Endocrinol.368(1–2), 59–70 (2013).
   PubMed Web of Science ®Google Scholar
• Ananthanarayanan M , LiY, SurapureddiSet al. Histone H3K4 trimethylation by MLL3 as part of ASCOM complex is critical for NR activation of bile acid transporter genes and is downregulated in cholestasis. Am. J. Physiol.300(5), G771 (2011).
   Google Scholar
• Kim YC , JungH, SeokSet al. MicroRNA-210 promotes bile acid–induced cholestatic liver injury by targeting mixed-lineage leukemia-4 methyltransferase in mice. Hepatology71(6), 2118–2134 (2020).
   PubMed Web of Science ®Google Scholar
• Li X , LiuR. Long non-coding RNA H19 in the liver-gut axis: A diagnostic marker and therapeutic target for liver diseases. Exp. Mol. Pathol.115, 104472 (2020).
   PubMed Web of Science ®Google Scholar
• Xiao Y , LiuR, LiXet al. Long noncoding RNA H19 contributes to cholangiocyte proliferation and cholestatic liver fibrosis in biliary atresia. Hepatology70(5), 1658–1673 (2019).
   PubMed Web of Science ®Google Scholar
• Zhang Y , LiuC, BarbierOet al. Bcl2 is a critical regulator of bile acid homeostasis by dictating Shp and lncRNA H19 function. Sci. Rep.6(1), 1–11 (2016).
   PubMed Web of Science ®Google Scholar
• Blumenberg M . Introductory chapter: transcriptome analysis. In: Transcriptome Analysis.BlumenbergM ( Ed.). IntechOpen, London, UK, 1–5 (2019).
   Google Scholar
• European Medicines Agency . Genomics genetics, transcriptomics and epigenetics subgroup report (2019).
   Google Scholar
• Schena M , ShalonD, DavisRW, BrownPO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (80-)270(5235), 467–470 (1995).
   PubMed Web of Science ®Google Scholar
• Yang X , KuiL, TangMet al. High-throughput transcriptome profiling in drug and biomarker discovery. Front. Genet.11, 19 (2020).
   PubMed Web of Science ®Google Scholar
• Mortazavi A , WilliamsBA, McCueK, SchaefferL, WoldB. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods5(7), 621–628 (2008).
   PubMed Web of Science ®Google Scholar
• Wang Z , GersteinM, SnyderM. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet.10(1), 57–63 (2009).
   PubMed Web of Science ®Google Scholar
• Blomme EAG , YangY, WaringJF. Use of toxicogenomics to understand mechanisms of drug-induced hepatotoxicity during drug discovery and development. Toxicol. Lett.186(1), 22–31 (2009).
   PubMed Web of Science ®Google Scholar
• de Longueville F , AtienzarFA, MarcqLet al. Use of a low-density microarray for studying gene expression patterns induced by hepatotoxicants on primary cultures of rat hepatocytes. Toxicol. Sci.75(2), 378–392 (2003).
   PubMed Web of Science ®Google Scholar
• Kienhuis AS , VitinsAP, PenningsJLAet al. Cyclosporine A treated in vitro models induce cholestasis response through comparison of phenotype-directed gene expression analysis of in vivo Cyclosporine A-induced cholestasis. Toxicol. Lett.221(3), 225–236 (2013).
   PubMed Web of Science ®Google Scholar
• Rodrigues RM , KolliparaL, ChaudhariUet al. Omics-based responses induced by bosentan in human hepatoma HepaRG cell cultures. Arch. Toxicol.92(6), 1939–1952 (2018).
   PubMed Web of Science ®Google Scholar
• Szalowska E , StoopenG, GrootMJ, HendriksenPJ, PeijnenburgAA. Treatment of mouse liver slices with cholestatic hepatotoxicants results in down-regulation of Fxr and its target genes. BMC Med. Genomics6, 39 (2013).
   PubMed Web of Science ®Google Scholar
• Van den Hof WFPM , CoonenMLJ, van HerwijnenMet al. Validation of gene expression profiles from cholestatic hepatotoxicants in vitro against human in vivo cholestasis. Toxicol. Vitr.44, 322–329 (2017).
   PubMed Web of Science ®Google Scholar
• Sun J , WangJ, ZhangN, YangR, ChenK, KongD. Identification of global mRNA expression profiles and comprehensive bioinformatic analyses of abnormally expressed genes in cholestatic liver disease. Gene.707, 9–21 (2019).
   PubMed Web of Science ®Google Scholar
• Ostrowski J , GorycaK, LazowskaIet al. Common functional alterations identified in blood transcriptome of autoimmune cholestatic liver and inflammatory bowel diseases. Sci. Rep.9(1), 7190 (2019).
   PubMedGoogle Scholar
• Baba N , KobashiH, YamamotoKet al. Gene expression profiling in biliary epithelial cells of primary biliary cirrhosis using laser capture microdissection and cDNA microarray. Transl. Res.148(3), 103–113 (2006).
   PubMed Web of Science ®Google Scholar
• Tabibian JH , TrussoniCE, O'HaraSP, SplinterPL, HeimbachJK, LaRussoNF. Characterization of cultured cholangiocytes isolated from livers of patients with primary sclerosing cholangitis. Lab. Investig.94(10), 1126–1133 (2014).
   PubMed Web of Science ®Google Scholar
• Li Q , GeX, XuX, ZhongY, QieZ. Comparison of the gene expression profiles between gallstones and gallbladder polyps. Int. J. Clin. Exp. Pathol.7(11), 8016–8023 (2014).
   PubMed Web of Science ®Google Scholar
• Yang B , LiuB, BiP, WuT, WangQ, ZhangJ. An integrated analysis of differential miRNA and mRNA expressions in human gallstones. Mol. Biosyst.11(4), 1004–1011 (2015).
   PubMed Web of Science ®Google Scholar
• Pertea M . The human transcriptome: an unfinished story. Genes (Basel).3(3), 344–360 (2012).
   PubMed Web of Science ®Google Scholar
• Vogel C , MarcotteEM. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet.13(4), 227–232 (2012).
   PubMed Web of Science ®Google Scholar
• Krishna RG , WoldF. Post-translational modification of proteins. Adv. Enzymol. Relat. Areas Mol. Biol.67, 265–298 (2006).
   Google Scholar
• Barrier M , MirkesPE. Proteomics in developmental toxicology. Reprod. Toxicol.19(Spec. Iss. 3), 291–304 (2005).
   PubMed Web of Science ®Google Scholar
• Nallagangula KS , ShashidharKN, LakshmaiahV, MuninarayanaC. Evolution of proteomic biomarker for chronic liver disease: Promise into reality. J. Circ. Biomarkers.7, 1849454418777186 (2018).
   Google Scholar
• Görg A , WeissW, DunnMJ. Current two-dimensional electrophoresis technology for proteomics. Proteomics.4(12), 3665–3685 (2004).
   PubMed Web of Science ®Google Scholar
• Mas VR , FisherRA, ArcherKJ, MalufDG. Proteomics and liver fibrosis: Identifying markers of fibrogenesis. Expert Rev. Proteomics.6(4), 421–431 (2009).
   PubMed Web of Science ®Google Scholar
• Ciocan-Cartita CA , JurjA, BuseMet al. The relevance of mass spectrometry analysis for personalized medicine through its successful application in cancer “Omics”. Int. J. Mol. Sci.20(10), 2576 (2019).
   PubMed Web of Science ®Google Scholar
• Timp W , TimpG. Beyond mass spectrometry, the next step in proteomics. Sci. Adv.6(2), doi:10.1126/sciadv.aax8978 (2020).
   PubMed Web of Science ®Google Scholar
• Chandramouli K , QianP-Y. Proteomics: challenges, techniques and possibilities to overcome biological sample complexity. Hum. Genomics Proteomics2009, 239204 (2009).
   PubMedGoogle Scholar
• Niu L , GeyerPE, MannM. Proteomics in the study of liver diseases. The Human Gut-Liver-Axis in Health and Disease, Springer (2018).
   Google Scholar
• Parent R , BerettaL. Proteomics in the study of liver pathology. J. Hepatol.43(1), 177–183 (2005).
   PubMed Web of Science ®Google Scholar
• Farina A , DelhayeM, LescuyerP, DumonceauJM. Bile proteome in health and disease. Compr. Physiol.4(1), 91–108 (2014).
   PubMed Web of Science ®Google Scholar
• Teng PN , BatemanNW, HoodBL, ConradsTP. Advances in proximal fluid proteomics for disease biomarker discovery. J. Proteome Res.9(12), 6091–6100 (2010).
   PubMed Web of Science ®Google Scholar
• Lankisch TO , MetzgerJ, NegmAAet al. Bile proteomic profiles differentiate cholangiocarcinoma from primary sclerosing cholangitis and choledocholithiasis. Hepatology53(3), 875–884 (2011).
   PubMed Web of Science ®Google Scholar
• Navaneethan U , LourdusamyV, VenkateshPGK, WillardB, SanakaMR, ParsiMA. Bile proteomics for differentiation of malignant from benign biliary strictures: A pilot study. Gastroenterol. Rep.3(2), 136–143 (2015).
   Google Scholar
• Metzger J , NegmAA, PlentzRRet al. Urine proteomic analysis differentiates cholangiocarcinoma from primary sclerosing cholangitis and other benign biliary disorders. Gut62(1), 122–130 (2013).
   PubMed Web of Science ®Google Scholar
• Barbhuiya MA , SahasrabuddheNA, PintoSMet al. Comprehensive proteomic analysis of human bile. Proteomics11(23), 4443–4453 (2011).
   PubMed Web of Science ®Google Scholar
• He F . Human liver proteome project: plan, progress, and perspectives. Mol. Cell. Proteomics4(12), 1841–1848 (2005).
   PubMed Web of Science ®Google Scholar
• Tyers M , MannM. From genomics to proteomics. Nature422(6928), 193–197 (2003).
   PubMed Web of Science ®Google Scholar
• Griffin JL , ShockcorJP. Metabolic profiles of cancer cells. Nat. Rev. Cancer4(7), 551–561 (2004).
   PubMed Web of Science ®Google Scholar
• Oliver SG . Functional genomics: lessons from yeast. Philos. Trans. R. Soc. B Biol. Sci.357(1417), 17–23 (2002).
   PubMed Web of Science ®Google Scholar
• Nicholson JK , LindonJC, HolmesE. “Metabonomics”: Understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica29(11), 1181–1189 (1999).
   PubMed Web of Science ®Google Scholar
• Beyoğlu D , IdleJR. Metabolomic and lipidomic biomarkers for premalignant liver disease diagnosis and therapy. Metabolites10(2), 50 (2020).
   PubMed Web of Science ®Google Scholar
• Nicholson JK , LindonJC. Systems biology: metabonomics. Nature.455, 1054–1056 (2008).
   PubMed Web of Science ®Google Scholar
• Sinclair K , DudleyE. Metabolomics and biomarker discovery. Adv. Exp. Med. Biol.1140, 613–633 (2019).
   PubMed Web of Science ®Google Scholar
• Yu M , ZhuY, CongQ, WuC. Metabonomics research progress on liver diseases. Can. J. Gastroenterol. Hepatol.2017, 8467192 (2017).
   PubMed Web of Science ®Google Scholar
• Gahlaut A , Vikas DahiyaMet al. Proteomics & metabolomics: mapping biochemical regulations. Drug Invent. Today.5(4), 321–326 (2013).
   Google Scholar
• Aoki M , KonyaY, TakagakiTet al. Metabolomic investigation of cholestasis in a rat model using ultra-performance liquid chromatography/tandem mass spectrometry. Rapid Commun. Mass Spectrom.25(13), 1847–1852 (2011).
   PubMed Web of Science ®Google Scholar
• Chen Z , ZhuY, ZhaoYet al. Serum metabolomic profiling in a rat model reveals protective function of paeoniflorin against ANIT induced cholestasis. Phyther. Res.30(4), 654–662 (2016).
   PubMed Web of Science ®Google Scholar
• Cho JY , MatsubaraT, KangDWet al. Urinary metabolomics in Fxr-null mice reveals activated adaptive metabolic pathways upon bile acid challenge. J. Lipid Res.51(5), 1063–1074 (2010).
   PubMed Web of Science ®Google Scholar
• Fu K , WangC, GaoYet al. Metabolomics and lipidomics reveal the effect of hepatic Vps33b deficiency on bile acids and lipids metabolism. Front. Pharmacol.10, 276 (2019).
   PubMed Web of Science ®Google Scholar
• Long Y , DongX, YuanYet al. Metabolomics changes in a rat model of obstructive jaundice: mapping to metabolism of amino acids, carbohydrates and lipids as well as oxidative stress. J. Clin. Biochem. Nutr.57(1), 50–59 (2015).
   PubMed Web of Science ®Google Scholar
• Yamazaki M , MiyakeM, SatoHet al. Perturbation of bile acid homeostasis is an early pathogenesis event of drug induced liver injury in rats. Toxicol. Appl. Pharmacol.268(1), 79–89 (2013).
   PubMed Web of Science ®Google Scholar
• Yang R , ZhaoQ, HuDD, XiaoXR, HuangJF, LiF. Metabolomic analysis of cholestatic liver damage in mice. Food Chem. Toxicol.120, 253–260 (2018).
   PubMed Web of Science ®Google Scholar
• Lian JS , LiuW, HaoSRet al. A serum metabolomic analysis for diagnosis and biomarker discovery of primary biliary cirrhosis and autoimmune hepatitis. Hepatobiliary Pancreat. Dis. Int.14(4), 413–421 (2015).
   PubMed Web of Science ®Google Scholar
• Bell LN , WulffJ, ComerfordM, VuppalanchiR, ChalasaniN. Serum metabolic signatures of primary biliary cirrhosis and primary sclerosing cholangitis. Liver Int.35(1), 263–274 (2015).
   PubMed Web of Science ®Google Scholar
• Trottier J , BiałekA, CaronPet al. Metabolomic profiling of 17 bile acids in serum from patients with primary biliary cirrhosis and primary sclerosing cholangitis: A pilot study. Dig. Liver Dis.44(4), 303–310 (2012).
   PubMedGoogle Scholar
• Vignoli A , OrlandiniB, TenoriLet al. Metabolic signature of primary biliary cholangitis and its comparison with celiac disease. J. Proteome Res.18(3), 1228–1236 (2019).
   PubMed Web of Science ®Google Scholar
• Chen X , ZhangX, XuBet al. The urinary bile acid profiling analysis of asymptomatic hypercholanemia of pregnancy: a pseudo-targeted metabolomics study. Clin. Chim. Acta497, 67–75 (2019).
   PubMed Web of Science ®Google Scholar
• Tang YM , WangJP, BaoWMet al. Urine and serum metabolomic profiling reveals that bile acids and carnitine may be potential biomarkers of primary biliary cirrhosis. Int. J. Mol. Med.36(2), 377–385 (2015).
   PubMed Web of Science ®Google Scholar
• Wishart DS , FeunangYD, MarcuAet al. HMDB 4.0: the human metabolome database for 2018. Nucleic Acids Res.46, D608–D617 (2018).
   PubMed Web of Science ®Google Scholar
• Beyoglu D , IdleJR. The metabolomic window into hepatobiliary disease. J. Hepatol.59(4), 842–858 (2013).
   PubMed Web of Science ®Google Scholar
• Ozer J , RatnerM, ShawM, BaileyW, SchomakerS. The current state of serum biomarkers of hepatotoxicity. Toxicology245(3), 194–205 (2008).
   PubMed Web of Science ®Google Scholar
• Pirola CJ , SookoianS. Multiomics biomarkers for the prediction of nonalcoholic fatty liver disease severity. World J. Gastroenterol.24(15), 1601–1615 (2018).
   PubMed Web of Science ®Google Scholar
• Schork N . Personalized medicine: time for one-person trials. Nature520(7549), 609–611 (2015).
   PubMed Web of Science ®Google Scholar
• Noor F . A shift in paradigm towards human biology-based systems for cholestatic-liver diseases. J. Physiol.593(23), 5043–5055 (2015).
   PubMed Web of Science ®Google Scholar
• Matthews H , HanisonJ, NirmalanN. “Omics”-informed drug and biomarker discovery: opportunities, challenges and future perspectives. Proteomes4(3), 28 (2016).
   PubMedGoogle Scholar
• Vinken M , LandesmannB, GoumenouMet al. Development of an adverse outcome pathway from drug-mediated bile salt export pump inhibition to cholestatic liver injury. Toxicol. Sci.136(1), 97–106 (2013).
   PubMed Web of Science ®Google Scholar
• Villeneuve DL , CrumpD, LiaGarcia-Reyero Net al. Adverse outcome pathway (AOP) development I: strategies and principles. Toxicol. Sci.142(2), 312–320 (2014).
   PubMed Web of Science ®Google Scholar
• Gijbels E , Vilas-BoasV, AnnaertP, VanhaeckeT, DevisscherL, VinkenM. Robustness testing and optimization of an adverse outcome pathway on cholestatic liver injury. Arch. Toxicol.94(4), 1151–1172 (2020).
   PubMed Web of Science ®Google Scholar
• Strimbu K , TavelJA. What are biomarkers?Curr. Opin. HIV AIDS5(6), 463–466 (2010).
   PubMed Web of Science ®Google Scholar