title: Microarray profiling shows distinct differences between primary tumors and commonly used preclinical models in hepatocellular carcinoma.
abstract: BACKGROUND
  Despite advances in therapeutics, outcomes for hepatocellular carcinoma (HCC) remain poor and there is an urgent need for efficacious systemic therapy. Unfortunately, drugs that are successful in preclinical studies often fail in the clinical setting, and we hypothesize that this is due to functional differences between primary tumors and commonly used preclinical models. In this study, we attempt to answer this question by comparing tumor morphology and gene expression profiles between primary tumors, xenografts and HCC cell lines.
  
  
  METHODS
  Hep G2 cell lines and tumor cells from patient tumor explants were subcutaneously (ectopically) injected into the flank and orthotopically into liver parenchyma of Mus Musculus SCID mice. The mice were euthanized after two weeks. RNA was extracted from the tumors, and gene expression profiling was performed using the Gene Chip Human Genome U133 Plus 2.0. Principal component analyses (PCA) and construction of dendrograms were conducted using Partek genomics suite.
  
  
  RESULTS
  PCA showed that the commonly used HepG2 cell line model and its xenograft counterparts were vastly different from all fresh primary tumors. Expression profiles of primary tumors were also significantly divergent from their counterpart patient-derived xenograft (PDX) models, regardless of the site of implantation. Xenografts from the same primary tumors were more likely to cluster together regardless of site of implantation, although heat maps showed distinct differences in gene expression profiles between orthotopic and ectopic models.
  
  
  CONCLUSIONS
  The data presented here challenges the utility of routinely used preclinical models. Models using HepG2 were vastly different from primary tumors and PDXs, suggesting that this is not clinically representative. Surprisingly, site of implantation (orthotopic versus ectopic) resulted in limited impact on gene expression profiles, and in both scenarios xenografts differed significantly from the original primary tumors, challenging the long-held notion that orthotopic PDX model is the gold standard preclinical model for HCC.
authors.affiliation: Cellular and Molecular Research, National Cancer Centre, Singapore, 169610, Singapore. wang.weining@u.duke.nus.edu.
authors.forename: Weining
authors.initials: W
authors.lastname: Wang
authors.affiliation: Cellular and Molecular Research, National Cancer Centre, Singapore, 169610, Singapore. gopaliyer@nccs.com.sg.|Department of Surgical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore. gopaliyer@nccs.com.sg.
authors.forename: N Gopalakrishna
authors.initials: NG
authors.lastname: Iyer
authors.affiliation: Department of General Surgery, Singapore General Hospital, 11 Hospital Drive, Singapore, 169608, Singapore. tay.hsien.tsung@sgh.com.sg.
authors.forename: Hsien Ts'ung
authors.initials: HT
authors.lastname: Tay
authors.affiliation: Cellular and Molecular Research, National Cancer Centre, Singapore, 169610, Singapore. yonghui.wu@duke-nus.edu.sg.
authors.forename: Yonghui
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Department of Histopathology, Singapore General Hospital, 11 Hospital Drive, Singapore, 169608, Singapore. lim.kiat.hon@sgh.com.sg.
authors.forename: Tony K H
authors.initials: TK
authors.lastname: Lim
authors.affiliation: SingHealth Experimental Medicine Centre (SEMC), Blk 9, Level 3, Outram Road, Singapore, 169608, Singapore. zheng.lin@singhealth.com.sg.
authors.forename: Lin
authors.initials: L
authors.lastname: Zheng
authors.affiliation: SingHealth Experimental Medicine Centre (SEMC), Blk 9, Level 3, Outram Road, Singapore, 169608, Singapore. song.in.chin@singhealth.com.sg.
authors.forename: In Chin
authors.initials: IC
authors.lastname: Song
authors.affiliation: Division of Information Systems, School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798, Singapore. asckkwoh@ntu.edu.sg.
authors.forename: Chee Keong
authors.initials: CK
authors.lastname: Kwoh
authors.affiliation: Laboratory of Molecular Endocrinology, Division of Molecular and Cellular Research, National Cancer Centre, 11 Hospital Drive, Singapore, 169610, Singapore. cmrhth@nccs.com.sg.
authors.forename: Hung
authors.initials: H
authors.lastname: Huynh
authors.affiliation: Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore. gmstanp@nus.edu.sg.
authors.forename: Patrick O B
authors.initials: PO
authors.lastname: Tan
authors.affiliation: Department of Surgical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore. pierce.chow@duke-nus.edu.sg.|Program in Translational and Clinical Liver Research, National Cancer Centre Singapore, Singapore, 169610, Singapore. pierce.chow@duke-nus.edu.sg.|Office of Clinical Sciences, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore. pierce.chow@duke-nus.edu.sg.
authors.forename: Pierce K H
authors.initials: PK
authors.lastname: Chow
mesh_terms: D000818:Animals; D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000473:pathology*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004195:Disease Models, Animal; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D056945:Hep G2 Cells; D064593:Heterografts; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000473:pathology*; D051379:Mice; D059467:Transcriptome