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Hypoxia Regulates Alternative Splicing of HIF and Non-HIF Target Genes

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Hypoxia Regulates Alternative Splicing of HIF and Non-HIF Target Genes Published OnlineFirst May 21, 2014; DOI: 10.1158/1541-7786.MCR-14-0149 Molecular Cancer Chromatin, Gene, and RNA Regulation Research Hypoxia Regulates Alternative Splicing of HIF and non-HIF Target Genes Johnny A. Sena1, Liyi Wang2, Lynn E. Heasley2, and Cheng-Jun Hu1,2 Abstract Hypoxia is a common characteristic of many solid tumors. The hypoxic microenvironment stabilizes hypoxia- inducible transcription factor 1a (HIF1a) and 2a (HIF2a/EPAS1) to activate gene transcription, which promotes tumor cell survival. The majority of human genes are alternatively spliced, producing RNA isoforms that code for functionally distinct proteins. Thus, an effective hypoxia response requires increased HIF target gene expression as well as proper RNA splicing of these HIF-dependent transcripts. However, it is unclear if and how hypoxia regulates RNA splicing of HIF targets. This study determined the effects of hypoxia on alternative splicing (AS) of HIF and non-HIF target genes in hepatocellular carcinoma cells and characterized the role of HIF in regulating AS of HIF- induced genes. The results indicate that hypoxia generally promotes exon inclusion for hypoxia-induced, but reduces exon inclusion for hypoxia-reduced genes. Mechanistically, HIF activity, but not hypoxia per se is found to be necessary and sufficient to increase exon inclusion of several HIF targets, including pyruvate dehydrogenase kinase 1 (PDK1). PDK1 splicing reporters confirm that transcriptional activation by HIF is sufficient to increase exon inclusion of PDK1 splicing reporter. In contrast, transcriptional activation of a PDK1 minigene by other transcription factors in the absence of endogenous HIF target gene activation fails to alter PDK1 RNA splicing. Implications: This study demonstrates a novel function of HIF in regulating RNA splicing of HIF target genes. Mol Cancer Res; 12(9); 1233–43. Ó2014 AACR. Introduction forms expression will be more informative than quantifying Hypoxia is a common characteristic of many solid tumors. total transcripts to appreciate the functional consequence of The hypoxic microenvironment stabilizes hypoxia-inducible gene regulation. transcription factor 1a (HIF1a) and 2a (HIF2a) that are Exon arrays contain probe sets interrogating every exon normally degraded under normoxia. The stabilized HIF1a of the transcriptome, thereby permitting the distinguish- and HIF2a proteins translocate to the nucleus, where they ing of different isoforms of a gene as well as measuring dimerize with aryl hydrocarbon receptor nuclear translocator gene expression levels. So far, two studies have examined (ARNT) to form HIF1a–ARNT (HIF1) and HIF2a– the effect of hypoxia in regulating RNA splicing using ARNT (HIF2) complexes. HIF1 and HIF2 activate gene exon arrays (6, 7). However, both studies used endothelia transcription to promote tumor progression and metastasis cells, a normal cell type. So far, hypoxia-mediated RNA (1–4). Thus, HIF-mediated transcriptional response is very splicing changes have not been measured in cancer cells. In important in cancer biology. addition, these previous studies in endothelial cells Recently, it was found that 95% of human genes are focused on non-HIF target genes and reported that hyp- alternatively spliced and RNA isoforms produced from a oxia, like other stresses, inhibits RNA splicing of non-HIF single gene code proteins with distinct or opposing functions target genes by promoting exon skipping and/or intron (5). Thus, it becomes increasingly clear that assessing iso- inclusion (6, 7). Thus, role of hypoxia in regulating RNA splicing of HIF-induced genes, the most important genes in hypoxia response is still unknown. Furthermore, none Authors' Affiliations: 1Molecular Biology Graduate Program and 2Depart- of these studies have addressed the molecular mechanisms ment of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado about how hypoxia regulates alternative splicing (AS) of HIF target genes. In this study, we used exon arrays to Note: Supplementary data for this article are available at Molecular Cancer Research Online (http://mcr.aacrjournals.org/). assess global effects of hypoxia on RNA splicing of HIF and non-HIF target genes in Hep3B cells, a cancer cell Corresponding Author: Cheng-Jun Hu, Department of Craniofacial Biol- ogy, School of Dental Medicine, University of Colorado Anschutz Medical line.Inaddition,westudiedifHIForhypoxiaper se is Campus, Aurora, CO 80045. Phone: 303-724-4574; Fax: 303-724-4580; important for RNA splicing of several HIF target genes. E-mail: [email protected] These findings have important implications for our under- doi: 10.1158/1541-7786.MCR-14-0149 standing of how HIFs promote tumorigenesis in response Ó2014 American Association for Cancer Research. to hypoxia. www.aacrjournals.org 1233 Downloaded from mcr.aacrjournals.org on September 29, 2021. © 2014 American Association for Cancer Research. Published OnlineFirst May 21, 2014; DOI: 10.1158/1541-7786.MCR-14-0149 Sena et al. Materials and Methods induced, (ii) genes that were predicted to undergo hypox- Cell culture ia-induced AS, and (iii) genes that were hypoxia induced and Hep3B cells were cultured in Minimum Essential Medi- exhibiting AS. um with Earle's Balanced Salt Solution (Hyclone) contain- Knockdown of endogenous mRNA using small ing 10% FBS, 2 mmol/L L-glutamine, 1 mmol/L sodium interfering RNAs pyruvate, 100,000 U/L penicillin/streptomycin, 1.5 g/L fi sodium bicarbonate, and 1Â nonessential amino acids Control (Qiagen; 1027281) or siRNAs speci c for human (NEAA). HEK293T, RCC4, RCC4T, and UM-SCC- ARNT (Qiagen; equal mix of SI00304220, SI00304234, fi and SI03020913), HIF1a (Qiagen; SI02664053), and 22B cells were grown in high-glucose Dulbecco's Modi ed a Eagle Medium (DMEM; Hyclone) with 10% FBS, 2 HIF2 (Qiagen; SI00380212) mRNAs were transfected into Hep3B cells at 40% confluency using HiPerFect mmol/L L-glutamine, 100,000 U/L penicillin/streptomycin, and 1Â NEAA. SK-N-MC cells were grown in RPMI-1640 Transfection Reagent (Qiagen) according to the manufac- turer's protocol. Thirty-two hours after transfection, cells (Hyclone) with 10% FBS, 2 mmol/L L-glutamine, 100,000 Â were cultured at 21% or 1.5% O2 for 12 to 16 hours and U/L penicillin/streptomycin, and 1 NEAA. Before hyp- fi oxia treatment, 25 mmol/L HEPES was added to growth then collected for mRNA or protein puri cation. media and cells were incubated under normoxia (21% O2)or hypoxia (1.5% O ) for 12 to 16 hours. All parental cell lines Viral transduction of Hep3B cells 2 The GFP-Flag, HIF1aTM-Flag (triple mutation to make were purchased from ATCC. After completing the experi- a ments, the parental (Hep3B, HEK293T, RCC4, UM-SCC- HIF protein active under normoxia, with Flag tag), and fi HIF2aTM-Flag lentiviral constructs were described (11). 22B, and SKNMC) and modi ed cell lines (RCC4T) were a a authenticated by DNA profiling or "fingerprinting" by the The GFP-Flag, HIF1 TM-Flag, or HIF2 TM-Flag plas- University of Colorado DNA Sequencing & Analysis Core. mid was cotransfected with psPAX2 packaging vector (Addgene), and pMD2.G envelope vector (Addgene) into HEK293T cells. Twenty-four hours after transfection, Exon array analysis of AS transfection media were replaced with complete Hep3B The genome-wide effect of hypoxia on AS was determined media. The following day, viral media were filtered to in Hep3B cells using the Affymetrix GeneChip Human remove possible 293T cells and viral particles were concen- Exon 1.0 ST array. Hep3B cells were cultured, as described trated using high-speed ultracentrifugation at 26,000 Âg for above, under normoxic (21%) or hypoxic (1.2%) conditions 3 hours. The viral pellet was resuspended in 1 mL of PBS and for 12 hours. RNA was prepared using a Qiagen RNeasy Plus added to 6 cm Hep3B cells (30% confluency) for 6 hours. RNA extraction kit. RNA was reverse transcribed and The following day, a second round of concentrated virus was assessed for hypoxic induction of HIF target genes using added to the same Hep3B cells. Twenty-four hours after the qPCR. RNAs that passed quality control were submitted to second viral transduction, Hep3B cells were harvested for the Gene Expression Core at the University of Colorado RNA and protein analysis. Comprehensive Cancer Center for exon array analysis. Three independent replicate samples were analyzed for each Plasmid constructs treatment. The Core performed target labeling, hybridiza- The CA9P/ADM, PAI1P/ADM, and PAI1PmHRE/ fi tion, and chip scanning. To assess AS events, raw CEL les ADM constructs were described previously (11). The were analyzed using the freely available AltAnalyze software CA9P/PDK1, PAI1P/PDK1, and PAI1PmHRE/PDK1 (http://www.altanalyze.org; ref. 8) with the following constructs were generated by replacing the ADM gene with settings: species, human; gene and exon set, both core; and PDK1 minigene that was PCR amplified from human gene and exon level normalization FIRMA. The array data genomic DNA and contained exon 3 to exon 5, including fi can be accessed at GEO (GSE57613). Raw CEL les were introns 3 and 4. The HIF1aTM-Flag, HIF2aTM-Flag, alternatively analyzed using easyExon (http://microarray. HIF1aDBD-Flag, HIF1aDBD/VP16-Flag, HIF1aDBD/ ym.edu.tw:8080/tools/module/easyexon/index.jsp?mod- E2F-Flag, and upstream stimulatory factor 2 (USF2) expres- ¼ fi e home), with default settings and using RMA ltering (9). sion plasmids were described previously (11–13). The G5/ In addition, AltAnalyze software was used for gene expres- PDK1 minigene was generated by replacing the ADM gene sion analysis. Genes predicted to undergo AS by AltAnalyze with PDK1 minigene in the G5/ADM construct that was and easyExon were then compared with genes that were described previously (11). The Gal4 DNA binding domain induced by hypoxia (AltAnalyze) using Venny (http:// (Gal4), Gal4/HIF1aTAD, Gal4/VP16, and Gal4/E2F1 bioinfogp.cnb.csic.es/tools/venny/) to identify genes that have been described in ref. (11). were predicted to undergo AS and hypoxia induction.
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