ORIGINAL ARTICLE A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas R Lin 1 , S Maeda 2 , C Liu 1 , M Karin 2 and TS Edgington 1 1 Department of Immunology, The Scripps Research Institute, La Jolla, CA, USA and 2 Laboratory of Gene Regulation and Signal Transduction, University of California, San Diego, La Jolla, CA, USA Tumor markers can facilitate understanding molecular cell biology of neoplasia and provide potential targets for the diagnosis and insight for intervention. We here identify a novel murine gene, hepcarcin (hcn), encoding a 7-kb mRNA-like transcript. The gene appears to be the murine ortholog of the human alpha gene, that is, MALAT-1. The gene and homologs lack credible open reading frames, consistent with a highly conserved large noncoding RNA (ncRNA). In all nodules of procarcinogen-induced murine hepatocellular carcinomas (HCCs) and human HCCs, expression was markedly elevated compared to the uninvolved liver. Quantitative analyses indicated a 6–7-fold increased RNA level in HCCs versus uninvolved liver, advancing this as a molecule of interest. This ncRNA was overexpressed in all five non-hepatic human carcinomas analysed, consistent with a potential marker for neoplastic cells and potential participant in the molecular cell biology of neoplasia. Oncogene (2007) 26, 851–858. doi:10.1038/sj.onc.1209846; published online 31 July 2006 Keywords: large noncoding RNA; carcinoma; hepcarcin; MALAT-1 Introduction Hepatocellular carcinoma (HCC) accounts for 84% of malignant hepatic neoplasms and ranks as the third most fatal form of neoplasia. HCC is associated with chronic inflammatory liver disease when also exposed to hepatocarcinogens (e.g. aflatoxin B1) or chronic infection with hepatitis viruses (hepatitis B virus (HBV) or hepatitis C virus). How the risk factors lead to HCC is complex and only partially elucidated. Recent cDNA microarray analyses have demonstrated in HCC deregulation of genes involved in cell cycle regulation and genes regulated by liver-enriched transcription factors (Xu et al., 2001a, b), implicating complex involvement of multiple regulatory pathways. Noncoding RNAs (ncRNAs) are abundant. Recently, numerous microRNAs (miRNAs), a class of small ncRNAs, have been identified and implicated in key roles in certain biological processes (Bartel, 2004). miRNAs are also linked to neoplastic transformation (Lu et al., 2005; Meltzer, 2005; Volinia et al., 2006). In addition, one type of ncRNAs transcribed from the introns of known genes correlate with the degree of differentiation of prostate cancer (Reis et al., 2004) or protect cells from Fas-mediated apoptosis (Yan et al., 2005). Another class of ncRNAs that have received relatively sparse attention are the large ncRNAs that, like mRNAs, are usually produced by RNA polymerase II, but lack significant and utilized open reading frames (ORFs). They appear to exert functional roles directly as ncRNAs and some have been identified to function as genetic regulators or riboregulators (Erdmann et al., 2001). Recent genomic and transcriptomic projects have unraveled an unexpectedly large number of large ncRNAs in the human (Scherer et al., 2003; Ota et al., 2004) and mouse (Okazaki et al., 2002; Carninci et al., 2005) genomes. The FANTOM consortium annotated 33 409 murine transcriptional units represent- ing 60 770 full-length cDNA sequences. Whereas about half (17 594) of the transcriptional units had coding potential, the other half (15 815) were candidate ncRNAs (Okazaki et al., 2002). Except for the clear difference between the percentage of unspliced/single exons for the transcripts, they were similar in terms of average length (1.9 kb for the noncoding versus 2.1 kb for the coding RNAs), and percentage of polyA tails and polyA signals. Some candidate ncRNAs in the collection were isolated from tissue-specific and stage- specific libraries, suggesting possible involvement in differentiation and development (Numata et al., 2003). Despite the existence of a sizable population of large ncRNAs, disproportionally few studies have investi- gated their functions. One of the better elucidated large ncRNAs is Xist ( X chromosome inactive specific transcript) that presents as a 17-kb (human) and a 15-kb (mouse) molecule responsible for somatic X-chromosome dosage compensation (Brockdorff et al., 1992; Brown et al., 1992; Plath et al., 2002). Another example is a paternally imprinted gene H19 (O’neill, 2005), with a conserved secondary structure but non-conserved ORFs, that functions as a tumor suppressor in some tumor types and may play a Received 12 May 2006; revised 20 June 2006; accepted 24 June 2006; published online 31 July 2006 Correspondence: Dr TS Edgington or Dr R Lin, Department of Immunology, The Scripps Research Institute, 10550 N. Torrey Pines Road, SP258, La Jolla, CA 92037, USA. E-mails: tse@scripps.edu and ruilin@scripps.edu Oncogene (2007) 26, 851–858 & 2007 Nature Publishing Group All rights reserved 0950-9232/07 $30.00 www.nature.com/onc