Springer Nature is making Coronavirus research free. View research | View latest news | Sign up for updates

Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets


Hepatocellular carcinoma (HCC) is an aggressive and deadly cancer. The molecular pathogenesis of the disease remains poorly understood. To better understand HCC biology and explore potential biomarkers and therapeutic targets, we investigated the whole transcriptome of HCC. Considering the genetic heterogeneity of HCC, four datasets from four studies consisting of 15 pairs of HCC and adjacent normal samples were analyzed. We observed that the number of lncRNAs expressed in each HCC sample was consistently greater than the adjacent normal sample. Moreover, 15 lncRNAs were identified expressed in five to seven HCC tissues but were not detected in any adjacent normal tissue. Differential expression analysis detected 35 up- and 80 down-regulated lncRNAs in HCC samples compared with adjacent normal samples. In addition, five differentially expressed lncRNAs were predicted to play a role in oxidation and reduction process. With regard to splicing alterations, we identified nine highly recurrent differential splicing events belonging to eight genes USO1, RPS24, CCDC50, THNSL2, NUMB, FN1 (two events), SLC39A14 and NR1I3. Of them, splicing alterations of SLC39A14 and NR1I3 were reported for the association with HCC for the first time. The splicing dysregulation in HCC may be influenced by three splicing factors ESRP2, CELF2 and SRSF5 which were significantly down-regulated in HCC samples. This study revealed uncharacterized aspects of HCC transcriptome and identified important lncRNAs and splicing isoforms with the potential to serve as biomarkers and therapeutic targets for the disease.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7


  1. Al-Ayoubi AM, Zheng H, Liu Y, Bai T, Eblen ST (2012) Mitogen-activated protein kinase phosphorylation of splicing factor 45 (SPF45) regulates SPF45 alternative splicing site utilization, proliferation, and cell adhesion. Mol Cell Biol 32:2880–2893

  2. Anders S, Pyl PT, Huber W (2015) HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169

  3. Bechara EG, Sebestyen E, Bernardis I, Eyras E, Valcarcel J (2013) RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation. Mol Cell 52:720–733

  4. Berasain C, Goni S, Castillo J, Latasa MU, Prieto J, Avila MA (2010) Impairment of pre-mRNA splicing in liver disease: mechanisms and consequences. World J Gastroenterol 16:3091–3102

  5. Berretta R, Moscato P (2010) Cancer biomarker discovery: the entropic hallmark. PLoS One 5:e12262

  6. Bi HS, Yang XY, Yuan JH, Yang F, Xu D, Guo YJ, Zhang L, Zhou CC, Wang F, Sun SH (2013) H19 inhibits RNA polymerase II-mediated transcription by disrupting the hnRNP U-actin complex. Biochim Biophys Acta 1830:4899–4906

  7. Biamonti G, Bonomi S, Gallo S, Ghigna C (2012) Making alternative splicing decisions during epithelial-to-mesenchymal transition (EMT). Cell Mol Life Sci 69:2515–2526

  8. Blagoev B, Ong SE, Kratchmarova I, Mann M (2004) Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 22:1139–1145

  9. Blaustein M, Pelisch F, Tanos T, Munoz MJ, Wengier D, Quadrana L, Sanford JR, Muschietti JP, Kornblihtt AR, Caceres JF, Coso OA, Srebrow A (2005) Concerted regulation of nuclear and cytoplasmic activities of SR proteins by AKT. Nat Struct Mol Biol 12:1037–1044

  10. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

  11. Borges L, Hsu ML, Fanger N, Kubin M, Cosman D (1997) A family of human lymphoid and myeloid Ig-like receptors, some of which bind to MHC class I molecules. J Immunol 159:5192–5196

  12. Braconi C, Kogure T, Valeri N, Huang N, Nuovo G, Costinean S, Negrini M, Miotto E, Croce CM, Patel T (2011) microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene 30:4750–4756

  13. Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest AR, Carninci P, Biffo S, Stupka E, Gustincich S (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491:454–457

  14. Chan TH, Lin CH, Qi L, Fei J, Li Y, Yong KJ, Liu M, Song Y, Chow RK, Ng VH, Yuan YF, Tenen DG, Guan XY, Chen L (2014) A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma. Gut 63:832–843

  15. Chang KH, Li R, Papari-Zareei M, Watumull L, Zhao YD, Auchus RJ, Sharifi N (2011) Dihydrotestosterone synthesis bypasses testosterone to drive castration-resistant prostate cancer. Proc Natl Acad Sci USA 108:13728–13733

  16. Chen Y, Riley DJ, Chen PL, Lee WH (1997) HEC, a novel nuclear protein rich in leucine heptad repeats specifically involved in mitosis. Mol Cell Biol 17:6049–6056

  17. Choesmel V, Fribourg S, Aguissa-Toure AH, Pinaud N, Legrand P, Gazda HT, Gleizes PE (2008) Mutation of ribosomal protein RPS24 in Diamond-Blackfan anemia results in a ribosome biogenesis disorder. Hum Mol Genet 17:1253–1263

  18. Choi EJ, Jang YJ, Cha EY, Shin JG, Lee SS (2013) Identification and characterization of novel alternative splice variants of human constitutive androstane receptor in liver samples of Koreans and Caucasians. Drug Metab Dispos 41:888–896

  19. Corrionero A, Minana B, Valcarcel J (2011) Reduced fidelity of branch point recognition and alternative splicing induced by the anti-tumor drug spliceostatin A. Genes Dev 25:445–459

  20. Crequer A, Picard C, Pedergnana V, Lim A, Zhang SY, Abel L, Majewski S, Casanova JL, Jablonska S, Orth G, Jouanguy E (2013) EVER2 deficiency is associated with mild T-cell abnormalities. J Clin Immunol 33:14–21

  21. Danan-Gotthold M, Golan-Gerstl R, Eisenberg E, Meir K, Karni R, Levanon EY (2015) Identification of recurrent regulated alternative splicing events across human solid tumors. Nucleic Acids Res 43:5130–5144

  22. David CJ, Manley JL (2010) Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes Dev 24:2343–2364

  23. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigo R (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–1789

  24. Ding C, Yang Z, Lv Z, Du C, Xiao H, Peng C, Cheng S, Xie H, Zhou L, Wu J, Zheng S (2015) Long non-coding RNA PVT1 is associated with tumor progression and predicts recurrence in hepatocellular carcinoma patients. Oncol Lett 9:955–963

  25. Dou Z, Ding X, Zereshki A, Zhang Y, Zhang J, Wang F, Sun J, Huang H, Yao X (2004) TTK kinase is essential for the centrosomal localization of TACC2. FEBS Lett 572:51–56

  26. Franklin RB, Levy BA, Zou J, Hanna N, Desouki MM, Bagasra O, Johnson LA, Costello LC (2012) ZIP14 zinc transporter downregulation and zinc depletion in the development and progression of hepatocellular cancer. J Gastrointest Cancer 43:249–257

  27. Ghigna C, Valacca C, Biamonti G (2008) Alternative splicing and tumor progression. Curr Genom 9:556–570

  28. Gill RB, Day A, Barstow A, Zaman G, Chenu C, Dhoot GK (2012) Mammalian Sulf1 RNA alternative splicing and its significance to tumour growth regulation. Tumour Biol 33:1669–1680

  29. Giulietti M, Piva F, D’Antonio M, D’Onorio De Meo P, Paoletti D, Castrignano T, D’Erchia AM, Picardi E, Zambelli F, Principato G, Pavesi G, Pesole G (2013) SpliceAid-F: a database of human splicing factors and their RNA-binding sites. Nucleic Acids Res 41:D125–D131

  30. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223–227

  31. Harn HJ, Ho LI, Yu CP, Wang MW, Lee HS, Lin JJ, Lee WH, Isola NR, Cooper DL (1994) The variant mRNA isoform of human metastasis gene (CD44 V) detected in the cell lines of human hepatocellular carcinoma. Biochem Mol Biol Int 32:233–238

  32. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigo R, Hubbard TJ (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22:1760–1774

  33. Hess C, Neri D (2015) The antibody-mediated targeted delivery of interleukin-13 to syngeneic murine tumors mediates a potent anticancer activity. Cancer Immunol Immunother

  34. Huang YF, Chang MD, Shieh SY (2009) TTK/hMps1 mediates the p53-dependent postmitotic checkpoint by phosphorylating p53 at Thr18. Mol Cell Biol 29:2935–2944

  35. Huang Q, Lin B, Liu H, Ma X, Mo F, Yu W, Li L, Li H, Tian T, Wu D, Shen F, Xing J, Chen ZN (2011) RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma. PLoS One 6:e26168

  36. Humphries MJ, Komoriya A, Akiyama SK, Olden K, Yamada KM (1987) Identification of two distinct regions of the type III connecting segment of human plasma fibronectin that promote cell type-specific adhesion. J Biol Chem 262:6886–6892

  37. Hynes R (1985) Molecular biology of fibronectin. Annu Rev Cell Biol 1:67–90

  38. Ishibashi M, Kogo R, Shibata K, Sawada G, Takahashi Y, Kurashige J, Akiyoshi S, Sasaki S, Iwaya T, Sudo T, Sugimachi K, Mimori K, Wakabayashi G, Mori M (2013) Clinical significance of the expression of long non-coding RNA HOTAIR in primary hepatocellular carcinoma. Oncol Rep 29:946–950

  39. Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, Barrette TR, Prensner JR, Evans JR, Zhao S, Poliakov A, Cao X, Dhanasekaran SM, Wu YM, Robinson DR, Beer DG, Feng FY, Iyer HK, Chinnaiyan AM (2015) The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 47:199–208

  40. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D (2011) Global cancer statistics. CA Cancer J Clin 61:69–90

  41. Kaida D, Motoyoshi H, Tashiro E, Nojima T, Hagiwara M, Ishigami K, Watanabe H, Kitahara T, Yoshida T, Nakajima H, Tani T, Horinouchi S, Yoshida M (2007) Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nat Chem Biol 3:576–583

  42. Kambara H, Gunawardane L, Zebrowski E, Kostadinova L, Jobava R, Krokowski D, Hatzoglou M, Anthony DD, Valadkhan S (2015) Regulation of interferon-stimulated gene BST2 by a lncRNA transcribed from a shared bidirectional promoter. Front Immunol 5:676

  43. Kamino H, Negishi M (2012) The nuclear receptor constitutive active/androstane receptor arrests DNA-damaged human hepatocellular carcinoma Huh7 cells at the G2/M phase. Mol Carcinog 51:206–212

  44. Kan Z, Zheng H, Liu X, Li S, Barber TD, Gong Z, Gao H, Hao K, Willard MD, Xu J, Hauptschein R, Rejto PA, Fernandez J, Wang G, Zhang Q, Wang B, Chen R, Wang J, Lee NP, Zhou W, Lin Z, Peng Z, Yi K, Chen S, Li L, Fan X, Yang J, Ye R, Ju J, Wang K, Estrella H, Deng S, Wei P, Qiu M, Wulur IH, Liu J, Ehsani ME, Zhang C, Loboda A, Sung WK, Aggarwal A, Poon RT, Fan ST, Wang J, Hardwick J, Reinhard C, Dai H, Li Y, Luk JM, Mao M (2013) Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res 23:1422–1433

  45. Kang L, Liu X, Gong Z, Zheng H, Wang J, Li Y, Yang H, Hardwick J, Dai H, Poon RT, Lee NP, Mao M, Peng Z, Chen R (2015) Genome-wide identification of RNA editing in hepatocellular carcinoma. Genomics 105:76–82

  46. Katz Y, Wang ET, Airoldi EM, Burge CB (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7:1009–1015

  47. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36

  48. Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP (2010) Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 3:ra8

  49. Kodama S, Koike C, Negishi M, Yamamoto Y (2004) Nuclear receptors CAR and PXR cross talk with FOXO1 to regulate genes that encode drug-metabolizing and gluconeogenic enzymes. Mol Cell Biol 24:7931–7940

  50. Konno Y, Negishi M, Kodama S (2008) The roles of nuclear receptors CAR and PXR in hepatic energy metabolism. Drug Metab Pharmacokinet 23:8–13

  51. Kotake Y, Sagane K, Owa T, Mimori-Kiyosue Y, Shimizu H, Uesugi M, Ishihama Y, Iwata M, Mizui Y (2007) Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat Chem Biol 3:570–575

  52. Kuznetsova EB, Kekeeva TV, Larin SS, Zemliakova VV, Babenko OV, Nemtsova MV, Zaletaev DV, Strel’nikov VV (2007) Novel methylation and expression markers associated with breast cancer. Mol Biol (Mosk) 41:624–633

  53. Lai MC, Yang Z, Zhou L, Zhu QQ, Xie HY, Zhang F, Wu LM, Chen LM, Zheng SS (2012) Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation. Med Oncol 29:1810–1816

  54. Lin ZY, Chuang WL (2012) Genes responsible for the characteristics of primary cultured invasive phenotype hepatocellular carcinoma cells. Biomed Pharmacother 66:454–458

  55. Lin B, Tan X, Liang J, Wu S, Liu J, Zhang Q, Zhu R (2014a) A reduction in reactive oxygen species contributes to dihydromyricetin-induced apoptosis in human hepatocellular carcinoma cells. Sci Rep 4:7041

  56. Lin KT, Shann YJ, Chau GY, Hsu CN, Huang CY (2014b) Identification of latent biomarkers in hepatocellular carcinoma by ultra-deep whole-transcriptome sequencing. Oncogene 33:4786–4794

  57. List T, Casi G, Neri D (2014) A chemically defined trifunctional antibody–cytokine–drug conjugate with potent antitumor activity. Mol Cancer Ther 13:2641–2652

  58. Liu B, Yao Z, Hu K, Huang H, Xu S, Wang Q, Yang Y, Ren J (2015) ShRNA-mediated silencing of the Ndc80 gene suppress cell proliferation and affected hepatitis B virus-related hepatocellular carcinoma. Clin Res Hepatol Gastroenterol

  59. Lu Y, Xu W, Ji J, Feng D, Sourbier C, Yang Y, Qu J, Zeng Z, Wang C, Chang X, Chen Y, Mishra A, Xu M, Lee MJ, Lee S, Trepel J, Linehan WM, Wang X, Yang Y, Neckers L (2015) Alternative splicing of the cell fate determinant Numb in hepatocellular carcinoma. Hepatology

  60. Matouk IJ, DeGroot N, Mezan S, Ayesh S, Abu-lail R, Hochberg A, Galun E (2007) The H19 non-coding RNA is essential for human tumor growth. PLoS One 2:e845

  61. Matsui S, Takahashi T, Oyanagi Y, Takahashi S, Boku S, Takahashi K, Furukawa K, Arai F, Asakura H (1997) Expression, localization and alternative splicing pattern of fibronectin messenger RNA in fibrotic human liver and hepatocellular carcinoma. J Hepatol 27:843–853

  62. Miao R, Luo H, Zhou H, Li G, Bu D, Yang X, Zhao X, Zhang H, Liu S, Zhong Y, Zou Z, Zhao Y, Yu K, He L, Sang X, Zhong S, Huang J, Wu Y, Miksad RA, Robson SC, Jiang C, Zhao Y, Zhao H (2014) Identification of prognostic biomarkers in hepatitis B virus-related hepatocellular carcinoma and stratification by integrative multi-omics analysis. J Hepatol 61:840–849

  63. Misquitta-Ali CM, Cheng E, O’Hanlon D, Liu N, McGlade CJ, Tsao MS, Blencowe BJ (2011) Global profiling and molecular characterization of alternative splicing events misregulated in lung cancer. Mol Cell Biol 31:138–150

  64. Nakajima H, Hirata A, Ogawa Y, Yonehara T, Yoda K, Yamasaki M (1991) A cytoskeleton-related gene, uso1, is required for intracellular protein transport in Saccharomyces cerevisiae. J Cell Biol 113:245–260

  65. Neumann O, Kesselmeier M, Geffers R, Pellegrino R, Radlwimmer B, Hoffmann K, Ehemann V, Schemmer P, Schirmacher P, Lorenzo Bermejo J, Longerich T (2012) Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors. Hepatology 56:1817–1827

  66. Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143:46–58

  67. Ou JJ, Wu F, Liang HJ (2010) Colorectal tumor derived fibronectin alternatively spliced EDA domain exserts lymphangiogenic effect on human lymphatic endothelial cells. Cancer Biol Ther 9:186–191

  68. Oyama F, Hirohashi S, Shimosato Y, Titani K, Sekiguchi K (1989) Deregulation of alternative splicing of fibronectin pre-mRNA in malignant human liver tumors. J Biol Chem 264:10331–10334

  69. Oyama F, Hirohashi S, Sakamoto M, Titani K, Sekiguchi K (1993) Coordinate oncodevelopmental modulation of alternative splicing of fibronectin pre-messenger RNA at ED-A, ED-B, and CS1 regions in human liver tumors. Cancer Res 53:2005–2011

  70. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413–1415

  71. Panzitt K, Tschernatsch MM, Guelly C, Moustafa T, Stradner M, Strohmaier HM, Buck CR, Denk H, Schroeder R, Trauner M, Zatloukal K (2007) Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA. Gastroenterology 132:330–342

  72. Parkin DM (2006) The global health burden of infection-associated cancers in the year 2002. Int J Cancer 118:3030–3044

  73. Pretto F, Elia G, Castioni N, Neri D (2014) Preclinical evaluation of IL2-based immunocytokines supports their use in combination with dacarbazine, paclitaxel and TNF-based immunotherapy. Cancer Immunol Immunother 63:901–910

  74. Radulescu AE, Mukherjee S, Shields D (2011) The Golgi protein p115 associates with gamma-tubulin and plays a role in Golgi structure and mitosis progression. J Biol Chem 286:21915–21926

  75. Rau A, Marot G, Jaffrezic F (2014) Differential meta-analysis of RNA-seq data from multiple studies. BMC Bioinform 15:91

  76. Ren S, Peng Z, Mao JH, Yu Y, Yin C, Gao X, Cui Z, Zhang J, Yi K, Xu W, Chen C, Wang F, Guo X, Lu J, Yang J, Wei M, Tian Z, Guan Y, Tang L, Xu C, Wang L, Gao X, Tian W, Wang J, Yang H, Wang J, Sun Y (2012) RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. Cell Res 22:806–821

  77. Robinson MD, Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11:R25

  78. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140

  79. Rybak JN, Roesli C, Kaspar M, Villa A, Neri D (2007) The extra-domain A of fibronectin is a vascular marker of solid tumors and metastases. Cancer Res 67:10948–10957

  80. Sahu A, Singhal U, Chinnaiyan AM (2015) Long noncoding RNAs in cancer: from function to translation. Trends Cancer 1:93–109

  81. Schrama D, Reisfeld RA, Becker JC (2006) Antibody targeted drugs as cancer therapeutics. Nat Rev Drug Discov 5:147–159

  82. Shiroishi M, Kuroki K, Rasubala L, Tsumoto K, Kumagai I, Kurimoto E, Kato K, Kohda D, Maenaka K (2006) Structural basis for recognition of the nonclassical MHC molecule HLA-G by the leukocyte Ig-like receptor B2 (LILRB2/LIR2/ILT4/CD85d). Proc Natl Acad Sci USA 103:16412–16417

  83. Shumway M, Cochrane G, Sugawara H (2010) Archiving next generation sequencing data. Nucleic Acids Res 38:D870–D871

  84. Snider NT, Altshuler PJ, Wan S, Welling TH, Cavalcoli J, Omary MB (2014) Alternative splicing of human NT5E in cirrhosis and hepatocellular carcinoma produces a negative regulator of ecto-5′-nucleotidase (CD73). Mol Biol Cell 25:4024–4033

  85. Sundin LJ, Guimaraes GJ, Deluca JG (2011) The NDC80 complex proteins Nuf2 and Hec1 make distinct contributions to kinetochore-microtubule attachment in mitosis. Mol Biol Cell 22:759–768

  86. Takei Y, Ishikawa S, Tokino T, Muto T, Nakamura Y (1998) Isolation of a novel TP53 target gene from a colon cancer cell line carrying a highly regulated wild-type TP53 expression system. Genes Chromosomes Cancer 23:1–9

  87. Taylor KM, Morgan HE, Johnson A, Nicholson RI (2005) Structure-function analysis of a novel member of the LIV-1 subfamily of zinc transporters, ZIP14. FEBS Lett 579:427–432

  88. Thorsen K, Mansilla F, Schepeler T, Oster B, Rasmussen MH, Dyrskjot L, Karni R, Akerman M, Krainer AR, Laurberg S, Andersen CL, Orntoft TF (2011) Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Mol Cell Proteom 10(M110):002998

  89. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329:689–693

  90. Uemura T, Shepherd S, Ackerman L, Jan LY, Jan YN (1989) Numb, a gene required in determination of cell fate during sensory organ formation in Drosophila embryos. Cell 58:349–360

  91. Vali L, Hahn O, Kupcsulik P, Drahos A, Sarvary E, Szentmihalyi K, Pallai Z, Kurucz T, Sipos P, Blazovics A (2008) Oxidative stress with altered element content and decreased ATP level of erythrocytes in hepatocellular carcinoma and colorectal liver metastases. Eur J Gastroenterol Hepatol 20:393–398

  92. Villa A, Trachsel E, Kaspar M, Schliemann C, Sommavilla R, Rybak JN, Rosli C, Borsi L, Neri D (2008) A high-affinity human monoclonal antibody specific to the alternatively spliced EDA domain of fibronectin efficiently targets tumor neo-vasculature in vivo. Int J Cancer 122:2405–2413

  93. Voth H, Oberthuer A, Simon T, Kahlert Y, Berthold F, Fischer M (2007) Identification of DEIN, a novel gene with high expression levels in stage IVS neuroblastoma. Mol Cancer Res 5:1276–1284

  94. Wang KC, Chang HY (2011) Molecular Mechanisms of Long Noncoding RNAs. Mol Cell 43:904–914

  95. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB (2008a) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476

  96. Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, Tempst P, Rosenfeld MG, Glass CK, Kurokawa R (2008b) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454:126–130

  97. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

  98. Wang F, Yuan JH, Wang SB, Yang F, Yuan SX, Ye C, Yang N, Zhou WP, Li WL, Li W, Sun SH (2014) Oncofetal long noncoding RNA PVT1 promotes proliferation and stem cell-like property of hepatocellular carcinoma cells by stabilizing NOP2. Hepatology 60:1278–1290

  99. Warzecha CC, Sato TK, Nabet B, Hogenesch JB, Carstens RP (2009) ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing. Mol Cell 33:591–601

  100. Wayner EA, Garcia-Pardo A, Humphries MJ, McDonald JA, Carter WG (1989) Identification and characterization of the T lymphocyte adhesion receptor for an alternative cell attachment domain (CS-1) in plasma fibronectin. J Cell Biol 109:1321–1330

  101. Wei P, Zhang J, Egan-Hafley M, Liang S, Moore DD (2000) The nuclear receptor CAR mediates specific xenobiotic induction of drug metabolism. Nature 407:920–923

  102. White ES, Sagana RL, Booth AJ, Yan M, Cornett AM, Bloomheart CA, Tsui JL, Wilke CA, Moore BB, Ritzenthaler JD, Roman J, Muro AF (2010) Control of fibroblast fibronectin expression and alternative splicing via the PI3K/Akt/mTOR pathway. Exp Cell Res 316:2644–2653

  103. Xiao Z, Ching Chow S, Han Li C, Chun Tang S, Tsui SK, Lin Z, Chen Y (2014) Role of microRNA-95 in the anticancer activity of Brucein D in hepatocellular carcinoma. Eur J Pharmacol 728:141–150

  104. Yamada KM (1989) Fibronectin domains and receptors. In: Mosher DF (ed) Fibronectin. Academic Press, San Diego, pp 47–121

  105. Yamazaki Y, Moore R, Negishi M (2011) Nuclear receptor CAR (NR1I3) is essential for DDC-induced liver injury and oval cell proliferation in mouse liver. Lab Invest 91:1624–1633

  106. Yan H, Yang Y, Zhang L, Tang G, Wang Y, Xue G, Zhou W, Sun S (2015) Characterization of the genotype and integration patterns of hepatitis B virus in early- and late-onset hepatocellular carcinoma. Hepatology

  107. Yochum GS, Cleland R, McWeeney S, Goodman RH (2007) An antisense transcript induced by Wnt/beta-catenin signaling decreases E2F4. J Biol Chem 282:871–878

  108. Young TL, Matsuda T, Cepko CL (2005) The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina. Curr Biol 15:501–512

  109. Yuan SX, Yang F, Yang Y, Tao QF, Zhang J, Huang G, Yang Y, Wang RY, Yang S, Huo XS, Zhang L, Wang F, Sun SH, Zhou WP (2012) Long noncoding RNA associated with microvascular invasion in hepatocellular carcinoma promotes angiogenesis and serves as a predictor for hepatocellular carcinoma patients poor recurrence-free survival after hepatectomy. Hepatology 56:2231–2241

  110. Zhang L, Yang F, Yuan JH, Yuan SX, Zhou WP, Huo XS, Xu D, Bi HS, Wang F, Sun SH (2013) Epigenetic activation of the MiR-200 family contributes to H19-mediated metastasis suppression in hepatocellular carcinoma. Carcinogenesis 34:577–586

  111. Zhang H, Ye J, Weng X, Liu F, He L, Zhou D, Liu Y (2015) Comparative transcriptome analysis reveals that the ECM-receptor interaction contributes to the venous metastases of hepatocellular carcinoma. Cancer Genet

  112. Zhao J, Zhao Y, Wang H, Gu X, Ji J, Gao C (2011) Association between metabolic abnormalities and HBV related hepatocelluar carcinoma in Chinese: a cross-sectional study. Nutr J 10:49

  113. Zhao J, Greene CM, Gray SG, Lawless MW (2014) Long noncoding RNAs in liver cancer: what we know in 2014. Expert Opin Ther Targets 18:1207–1218

  114. Zhuo H, Tang J, Lin Z, Jiang R, Zhang X, Ji J, Wang P, Sun B (2015) The aberrant expression of MEG3 regulated by UHRF1 predicts the prognosis of hepatocellular carcinoma. Mol Carcinog

Download references


This research was sponsored by Merck Sharp & Dohme (MSD) postdoc fellowship. We thank I-Ming Wang for good comments and Yunfei Pei, Hongchao Lu and Lan Chen for valuable discussion.

Author information

Correspondence to Xuegong Zhang or Ronghua Chen.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

For this type of study formal consent is not required.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLSX 87 kb)

Supplementary material 2 (PDF 3033 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Zhang, L., Liu, X., Zhang, X. et al. Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets. Mol Genet Genomics 291, 1035–1051 (2016).

Download citation


  • HCC
  • Long noncoding RNA (lncRNA)
  • Alternative splicing
  • RNA-Seq