Date Published: February 1, 2018
Publisher: Public Library of Science
Author(s): Yating Cheng, Parisa Imanirad, Indira Jutooru, Erik Hedrick, Un-Ho Jin, Aline Rodrigues Hoffman, Jeann Leal de Araujo, Benjamin Morpurgo, Andrei Golovko, Stephen Safe, Surinder K. Batra.
Metastasis-associated lung adenocarcinoma transcript-1 (MALAT-1) is a long non-coding RNA (lncRNA) that is a negative prognostic factor for patients with pancreatic cancer and several other tumors. In this study, we show that knockdown of MALAT-1 in Panc1 and other pancreatic cancer cell lines decreases cell proliferation, survival and migration. We previously observed similar results for the lncRNAs HOTTIP and HOTAIR in Panc1 cells; however, RNAseq comparison of genes regulated by MALAT-1 shows minimal overlap with HOTTIP/HOTAIR-regulated genes. Analysis of changes in gene expression after MALAT-1 knockdown shows that this lncRNA represses several tumor suppressor-like genes including N-myc downregulated gene-1 (NDRG-1), a tumor suppressor in pancreatic cancer that is also corepressed by EZH2 (a PRC2 complex member). We also observed that Specificity proteins Sp1, Sp3 and Sp4 are overexpressed in Panc1 cells and Sp knockdown or treatment with small molecules that decrease Sp proteins expression also decrease MALAT-1 expression. We also generated Kras-overexpressing p53L/L;LSL-KrasG12DL/+;p48Cre+/- (p53L/L/KrasG12D) and p53L/+;LSLKrasG12DL/+;p48Cre+/- (p53L/+/KrasG12D) mice which are p53 homo- and heterozygous, respectively. These mice rapidly develop pancreatic ductal adenocarcinoma-like tumors and were crossed with MALAT-1-/- mice. We observed that the loss of one or two MALAT-1 alleles in these Ras overexpressing mice does not significantly affect the time to death; however, the loss of MALAT-1 in the p53-/+ (heterozygote) mice slightly increases their lifespan.
Results of high throughput sequencing technologies show that less than 2% of the human genome encodes for proteins, whereas up to 75% of the genome transcribes non-coding RNAs (ncRNAs) which are highly variable in length, function and regulation . MicroRNAs (miRNAs) are 21–23 bp in length and there is evidence showing that miRNAs play important roles in maintaining cellular homeostasis and in diseases such as cancer through their sequence-specific regulation (primarily repression) of genes [2, 3]. There is also evidence that long ncRNAs (lncRNAs) >200 bp play an equally important role in normal cell functions and disease, and estimations from the Encyclopedia of DNA Element Project Consortium indicate that the human genome contains up to 16,000 genes encoding 28,000 lncRNA transcripts .
MALAT-1 expression in many tumors is a negative prognostic factor for patients, and results obtained in this study and previous reports confirm that MALAT-1 is a pro-oncogenic factor for pancreatic cancer (Fig 1). We have previously reported that the lncRNAs HOTAIR and HOTTIP regulate expression of genes associated with pancreatic cancer cell proliferation, survival and migration [37, 38]. A comparison of genes regulated by MALAT-1 and HOTTIP and HOTAIR in Panc1 cells indicates <6% overlap in coregulated genes, and similar results were observed after comparing specific gene sets associated with proliferation, survival and migration (Fig 3B–3D). APAF1 is an example of a gene regulated (suppressed) by MALAT-1 and not HOTAIR or HOTTIP, and APAF1 induction after MALAT-1 knockdown plays an important role in activating apoptosis and other pathways in Panc1 cells (Fig 4B). Interestingly, although MALAT-1, HOTAIR and HOTTIP exhibit similar functional pro-oncogenic activities in pancreatic cancer cells (Fig 1), the targeted (RNAi) loss of any one of these lncRNAs cannot be rescued by the other two lncRNAs and this supports the array data showing their regulation of different sets of genes, and we are currently investigating the functions of key genes differentially regulated by MALAT-1, HOTTIP and HOTAIR. Source: http://doi.org/10.1371/journal.pone.0192264