Abstract
The long non-coding RNAs (lncRNAs) are matter of intense investigation as potential regulators of gene expression. In the case of the transglutaminase 2 gene (TGM2) the databases of genome sequence indicate location of a lncRNA (LOC107987281) within the first intron. This lncRNA is 1000 bp long, arises from 2 exons and starts few nucleotides 3′ of the first splicing site of translated TGM2. We have analysed correlations between expression of LOC107987281 lncRNA and TGM2 mRNA by real-time PCR in K562 cell line untreated or treated with the anticancer drugs TPA (12-O-tetradecanoylphorbol-13-acetate), Docetaxel and Doxorubicin. In the treated cells the lncRNA increase follows the trend of TGM2 transcript. To validate this finding we used HumanExon1_0ST Affymetrix; chip data were background-adjusted, quantile-normalized and summarized using robust multi-array average analysis implemented in the R package. The probesets recognize sequences inside each exon, near intronic splicing sites and others located in the untranslated regions of TGM2 gene. The analysis of total RNA samples in GEO datasets from K562, HL-60, THP-1 and U937 cell lines, untreated or treated with TPA in replicated experiments confirmed our earlier results. These demonstrate correlation between LOC107987281 and TGM2 mRNA in the cell lines (K562, HL60 and THP-1) where increased levels of TGM2 mRNA are produced. Additional array study on 358 samples of several normal and paired tumor tissues leads to the same conclusions, indicating a correlation between full-length TGM2 mRNA and LOC107987281 lncRNA in relation to the development of several tumors.
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Abbreviations
- AD:
-
Alzheimer’s disease
- ATRA:
-
All-trans-retinoic acid
- DMSO:
-
Dimethyl sulfoxide
- GEO:
-
Gene Expression Omnibus
- HD:
-
Huntington’s disease
- HPRT1:
-
Hypoxanthine phosphoribosyltransferase
- lncRNA:
-
Long non-coding RNA
- miRNA:
-
microRNA
- NI:
-
Normalized intensity
- PLCδ1:
-
Phospholipase Cδ1
- RMA:
-
Robust multi-array average
- RT-qPCR:
-
Reverse Transcription- quantitative Polymerase Chain Reaction
- SI:
-
Splicing index
- SPSS:
-
Statistical package for social science
- TPA:
-
12-O-Tetradecanoylphorbol-13-acetate
- TGH:
-
Transglutaminase 2 isoform AA1-548
- TGH2:
-
Transglutaminase 2 isoform AA1-349
- TGM2 :
-
Transglutaminase 2 gene
- tTGV1 :
-
tTG alternative splicing variant 1
- tTGV2 :
-
tTG alternative splicing variant 2
- Tg2:
-
Type 2 transglutaminase
- NT:
-
Untreated
References
Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J (2008) Gene expression and isoform variation analysis using Affymetrix exon arrays. BMC Genom 9:529–545. https://doi.org/10.1186/1471-2164-9-529
Bengtsson H, Simpson K, Bullard J, Hansen K (2008) Aroma.affymetrix: a generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory. Tech Rep 745. Department of Statistics, University of California, Berkeley
Beninati S, Piacentini M, Bergamini CM (2017) Transglutaminase 2, a double face enzyme. Amino Acids 49:415–423. https://doi.org/10.1007/s00726-017-2394-5
Bergamini CM, Collighan RJ, Wang Z, Griffin M (2011) Structure and regulation of type 2 transglutaminase in relation to its physiological functions and pathological roles. Adv Enzymol Relat Areas Mol Biol 78:1–46
Bhakat KK, Izumi T, Yang SH, Hazra TK, Mitra S (2003) Role of acetylated human AP-endonuclease (APE1/Ref-1) in regulation of the parathyroid hormone gene. EMBO J 22:6299–6309. https://doi.org/10.1093/emboj/cdg595
Breitman TR, Selonick SE, Collins SJ (1980) Induction of differentiation of the human promyelocytic leukemia cell line (HL-60) by retinoic acid. Proc Natl Acad Sci USA 77:2936–2940
Buske FA, Bauer DC, Mattick JS, Bailey TL (2012) Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data. Genome Res 22:1372–1381. https://doi.org/10.1101/gr.130237.111
Chhabra A, Verma A, Mehta K (2009) Tissue transglutaminase promotes or suppresses tumors depending on cell context. Anticancer Res 29:1909–1919
Cho SY, Jeong EM, Lee JH, Kim HJ, Lim J, Kim CW, Shin DM, Jeon JH, Choi K, Kim IG (2012) Doxorubicin induces the persistent activation of intracellular transglutaminase 2 that protects from cell death. Mol Cells 33:235–241. https://doi.org/10.1007/s10059-012-2201-9
Citron BA, SantaCruz KS, Daviesi PJA, Festoff BW (2001) Intron-exon swapping of transglutaminase mRNA and neuronal Tau aggregation in Alzheimer’s disease. J Biol Chem 276:3295–32301. https://doi.org/10.1074/jbc.M004776200
Cook KD, Miller J (2010) TCR-dependent translational control of GATA-3 enhances Th2 differentiation. J Immunol 185:3209–3216. https://doi.org/10.4049/jimmunol.0902544. (Epub 2010 Aug 9)
Costa FF (2005) Non-coding RNAs: new players in eukaryotic biology. Gene 357:83–94. https://doi.org/10.1016/j.gene.2005.06.019
Daniel B, Nagy G, Hah N, Horvath A, Czimmerer Z, Poliska S, Gyuris T, Keirsse J, Gysemans C, van Ginderachter JA, Balint BL, Evans RM, Barta E, Nagy L (2014) The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages. Genes Dev 28:1562–1577. https://doi.org/10.1101/gad.242685.114
Eckert RL, Kaartinen MT, Nurminskaya M, Belkin AM, Colak G, Johnson GV, Mehta K (2014) Transglutaminase regulation of cell function. Physiol Rev 94:383–417. https://doi.org/10.1152/physrev.00019.2013
Eckert RL, Fisher ML, Grun D, Adhikary G, Xu W, Kerr C (2015) Transglutaminase is a tumor cell and cancer stem cell survival factor. Mol Carcinog 54:947–958. https://doi.org/10.1002/mc.22375
Eom S, Kim Y, Kim M, Park D, Lee H, Lee YS, Choe J, Kim YM, Jeoung D (2014) Transglutaminase II/microRNA-218/-181a loop regulates positive feedback relationship between allergic inflammation and tumor metastasis. J Biol Chem 289:29483–29505. https://doi.org/10.1074/jbc.M114.603480
Fagerberg L, Hallstrӧm BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S, Danielsson A, Edlund K, Asplund A, Sjӧstedt E, Szigyarto CAH, Skogs M, Takanen JO, Berling H, Tegel H, Mulder J, Nilsson P, Schwenk JM, Lindskog C, Danielsson F, Mardinoglu A, Sivertsson A, Feilitzen K, Forsberg M, Olsson I, Navani S, Huss M, Nielsen J, Ponten F, Uhlén M (2014) Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteom 13:397–406. https://doi.org/10.1074/mcp.m113.035600
Fatima R, Akhade VS, Pal D, Rao SM (2015) Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets. Mol Cell Ther 3:5–24. https://doi.org/10.1186/s40591-015-0042-6
Fraij BM, Gonzales RA (1996) A third human tissue transglutaminase homologue as a result of alternative gene transcripts. Biochim Biophys Acta 1306:63–74
Gangemi RMR, Santamaria B, Bargellesi A, Cosulich E, Fabbi M (2000) Late apoptotic effects of taxanes on K562 erythroleukemia cells: apoptosis is delayed upstream of caspase-3 activation. Int J Cancer 85:527–533. https://doi.org/10.1002/(SICI)1097-0215(20000215)85:4%3c527::AID-IJC14%3e3.0.CO;2-%23
GeneChip® Exon Arrays Technical Note (2017) Identifying and validating alternative splicing events. https://tools.thermofisher.com/content/sfs/brochures/id_altsplicingevents_technote.pdf
Hasselgren PO (2007) Ubiquitination, phosphorylation, and acetylation—triple threat in muscle wasting. J Cell Physiol 213:679–689. https://doi.org/10.1002/jcp.21190
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39:311–318. https://doi.org/10.1038/ng1966
Ho VW, Hofs E, Elisia I, Lam V, Hsu BE, Lai J, Luk B, Samudio I, Krystal G (2016) All trans retinoic acid, transforming growth factor β and prostaglandin E2 in mouse plasma synergize with basophil-secreted interleukin-4 to M2 polarize murine macrophages. PLoS One 11:e0168072. https://doi.org/10.1371/journal.pone.0168072
Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A (2007) A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genom 8:39–55. https://doi.org/10.1186/1471-2164-8-39
Karpuj MV, Garren H, Slunt H, Price DL, Gusella J, Becher MW, Steinman L (1999) Transglutaminase aggregates huntingtin into nonamyloidogenic polymers, and its enzymatic activity increases in Huntington’s disease brain nuclei. Proc Natl Acad Sci USA 96:7388–7393
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D (2002) UCSC genome browser: the human genome browser at UCSC. Genome Res 12:996–1006. https://doi.org/10.1101/gr.229102
Kim JH, Nam KH, Kwon OS, Kim IG, Bustin M, Choy HE, Park SC (2002) Histone cross-linking by transglutaminase. Biochem Biophys Res Commun 293:1453–1457
Király R, Demény M, Fésüs L (2011) Protein transamidation by transglutaminase 2 in cells: a disputed Ca2+-dependent action of a multifunctional protein. FEBS J 278:4717–4739. https://doi.org/10.1111/j.1742-4658.2011.08345.x
Király R, Barta E, Fésüs L (2013) Polymorphism of transglutaminase 2: unusually low frequency of genomic variants with deficient functions. Amino Acids 44:215–225. https://doi.org/10.1007/s00726-011-1194-6
Kitamura H, Kimura S, Shimamoto Y, Okabe J, Ito M, Miyamoto T, Naoe Y, Kikuguchi C, Meek B, Toda C, Okamoto S, Kanehira K, Hase K, Watarai H, Ishizuka M, El-Osta A, Ohara O, Miyoshi I (2013) Ubiquitin-specific protease 2–69 in macrophages potentially modulates metainflammation. FASEB J 27:4940–4953. https://doi.org/10.1096/fj.13-233528
Kumar S, Mehta K (2012) Tissue transglutaminase constitutively activates HIF-1α promoter and nuclear factor-κB via a non-canonical pathway. PLoS One 7(11):e49321. https://doi.org/10.1371/journal.pone.0049321
Kuo TF, Tatsukawa H, Kojima S (2011) New insights into the functions and localization of nuclear transglutaminase 2. FEBS J 278:4756–4767. https://doi.org/10.1111/j.1742-4658.2011.08409.x
Lai TS, Greenberg CS (2013) TGM2 and implications for human disease: role of alternative splicing. Front Biosci (Landmark Ed) 18:504–519
Lai TS, Liu Y, Li W, Greenberg CS (2007) Identification of two GTP-independent alternatively spliced forms of tissue transglutaminase in human leukocytes, vascular smooth muscle, and endothelial cells. FASEB J 21:4131–4143. https://doi.org/10.1096/fj.06-7598com
Lam MT, Li W, Rosenfeld MG, Glass CK (2014) Enhancer RNAs and regulated transcriptional programs. Trends Biochem Sci 39:170–182. https://doi.org/10.1016/j.tibs.2014.02.007
Lee J, Kim YS, Choi DH, Bang MS, Han TR, Joh TH, Kim SY (2004) Transglutaminase 2 induces nuclear factor-kB activation via a novel pathway in BV-2 microglia. J Biol Chem 279:53725–53735. https://doi.org/10.1074/jbc.M407627200
Lee EJ, Park MK, Kim HJ, Kang JH, Kim YR, Kang GJ, Byun HJ, Lee CH (2014) 12-O-Tetradecanoylphorbol-13-acetate induces keratin 8 phosphorylation and reorganization via expression of transglutaminase-2. Biomol Ther 22:122–128. https://doi.org/10.4062/biomolther.2014.007
Liu T, Tee AE, Porro A, Smith SA, Dwarte T, Liu PY, Iraci N, Sekyere E, Haber M, Norris MD, Diolaiti D, Della Valle G, Perini G, Marshall GM (2007) Activation of tissue transglutaminase transcription by histone deacetylase inhibition as a therapeutic approach for Myc oncogenesis. Proc Natl Acad Sci USA 104:18682–18687. https://doi.org/10.1073/pnas.0705524104
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25:402–408. https://doi.org/10.1006/meth.2001.1262
Lu S, Davies PJ (1997) Regulation of the expression of the tissue transglutaminase gene by DNA methylation. Proc Natl Acad Sci USA 94:4692–4697
Mann AP, Verma A, Sethi G, Manavathi B, Wang H, Fok JY, Kunnumakkara AB, Kumar R, Aggarwal BB, Mehta K (2006) Overexpression of tissue transglutaminase leads to constitutive activation of nuclear factor-{kappa}B in cancer cells: delineation of a novel pathway. Cancer Res 66:8788–8795. https://doi.org/10.1158/0008-5472.CAN-06-1457
Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445:666–670. https://doi.org/10.1038/nature05519
Martinez FO, Helming L, Milde R, Varin A, Melgert BN, Draijer C, Thomas B, Fabbri M, Crawshaw A, Ho LP, Ten Hacken NH, Cobos Jiménez V, Kootstra NA, Hamann J, Greaves DR, Locati M, Mantovani A, Gordon S (2013) Genetic programs expressed in resting and IL-4 alternatively activated mouse and human macrophages: similarities and differences. Blood 121:e57–e69. https://doi.org/10.1182/blood-2012-06-436212
Mattick JS (2004) RNA regulation: a new genetics? Nat Rev Genet 5:316–323. https://doi.org/10.1038/nrg1321
Mehta K, Fok J, Miller FR, Koul D, Sahin AA (2004) Prognostic significance of tissue transglutaminase in drug resistant and metastatic breast cancer. Clin Cancer Res 10:8068–8076. https://doi.org/10.1158/1078-0432.CCR-04-1107
Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Léveillé N, Kalluri R, de Laat W, Agami R (2013) eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 49:524–535. https://doi.org/10.1016/j.molcel.2012.11.021
Mirza A, Liu SL, Frizell E, Zhu J, Maddukuri S, Martinez J, Davies P, Schwarting R, Norton P, Zern MA (1997) A role for tissue transglutaminase in hepatic injury and fibrogenesis, and its regulation by NF-kappaB. Am J Physiol 272:G281–G288
Ozpolat B, Akar U, Steiner M, Zorrilla-Calancha I, Tirado-Gomez M, Colburn N, Danilenko M, Kornblau S, Lopez-Berestein G (2007) Programmed cell death-4 tumor suppressor protein contributes to retinoic acid-induced terminal granulocytic differentiation of human myeloid leukemia cells. Mol Cancer Res 5:95–108. https://doi.org/10.1158/1541-7786.MCR-06-0125
Ozpolat B, Akar U, Tekedereli I, Alpay SN, Barria M, Gezgen B, Zhang N, Coombes K, Kornblau S, Lopez-Berestein G (2012) PKCδ regulates translation initiation through PKR and eIF2α in response to retinoic acid in acute myeloid leukemia cells. Leuk Res Treat 482905:1–17. https://doi.org/10.1155/2012/482905
Pencovich N, Jaschek R, Tanay A, Groner Y (2011) Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models. Blood 117:e1–e114. https://doi.org/10.1182/blood-2010-07-295113
Phatak VM, Croft SM, Rameshaiah Setty SG, Scarpellini A, Hughes DC, Rees R, McArdle S, Verderio EAM (2013) Expression of transglutaminase-2 isoforms in normal human tissues and cancer cell lines: dysregulation of alternative splicing in cancer. Amino Acids 44:33–44. https://doi.org/10.1007/s00726-011-1127-4
Prasanth KV, Spector DL (2007) Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum. Genes Dev 21:11–42. https://doi.org/10.1101/gad.1484207
Purdom E, Simpson KM, Robinson MD, Conboy JG, Lapuk AV, Speed TP (2008) FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics 24:1707–1714. https://doi.org/10.1093/bioinformatics/btn284
Sándor K, Daniel B, Kiss B, Kovács F, Szondy Z (2016) Transcriptional control of transglutaminase 2 expression in mouse apoptotic thymocytes. Biochim Biophys Acta 1859:964–974. https://doi.org/10.1016/j.bbagrm.2016.05.011
Shrestha R, Tatsukawa H, Shrestha R, Ishibashi N, Matsuura T, Kagechika H, Kose S, Hitomi K, Imamoto N, Kojima S (2015) Molecular mechanism by which acyclic retinoid induces nuclear localization of transglutaminase 2 in human hepatocellular carcinoma cells. Cell Death Dis 6:e2002. https://doi.org/10.1038/cddis.2015.339
Signal B, Gloss BS, Dinger ME (2016) Computational approaches for functional prediction and characterisation of long noncoding RNAs. Trends Genet 32:620–637. https://doi.org/10.1016/j.tig.2016.08.004
Stamnaes J, Pinkas DM, Fleckenstein B, Khosla C, Sollid LM (2010) Redox regulation of transglutaminase 2 activity. J Biol Chem 285:25402–25409. https://doi.org/10.1074/jbc.M109.097162
Suedhoff T, Birckbichler PJ, Lee KN, Conway E, Patterson MK Jr (1990) Differential expression of transglutaminase in human erythroleukemia cells in response to retinoic acid. Cancer Res 50:7830–7834
Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J (2005) A new frontier for molecular medicine: noncoding RNAs. Biochim Biophys Acta 1756:65–75. https://doi.org/10.1016/j.bbcan.2005.07.005
Takaku M, Grimm SA, Wade PA (2015) GATA3 in breast cancer: tumor suppressor or oncogene? Gene Expr 16:163–168. https://doi.org/10.3727/105221615X14399878166113
Tatsukawa H, Furutani Y, Hitomi K, Kojima S (2016) Transglutaminase 2 has opposing roles in the regulation of cellular functions as well as cell growth and death. Cell Death Dis 7:e2244. https://doi.org/10.1038/cddis.2016.150
Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, Blencowe BJ, Prasanth SG, Prasanth KV (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39:925–938. https://doi.org/10.1016/j.molcel.2010.08.011
Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, Glass CK, Rosenfeld MG, Fu XD (2011) Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474:390–394. https://doi.org/10.1038/nature10006
Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z (2013) Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res 41:D171–D176. https://doi.org/10.1093/nar/gks1221
Yan C, Boyd DD (2006) Histone H3 acetylation and H3 K4 methylation define distinct chromatin regions permissive for transgene expression. Mol Cell Biol 26:6357–6371. https://doi.org/10.1128/MCB.00311-06
Yao XH, Nyomba BL (2008) Hepatic insulin resistance induced by prenatal alcohol exposure is associated with reduced PTEN and TRB3 acetylation in adult rat offspring. Am J Physiol Regul Integr Comp Physiol 294:R1797–R1806. https://doi.org/10.1152/ajpregu.00804.2007
Zhang J, Lesort M, Guttmann RP, Johnson GV (1998) Modulation of the in situ activity of tissue transglutaminase by calcium and GTP. J Biol Chem 273:2288–2295
Acknowledgements
S.V. is supported by Associazione Italiana Ricerca sul Cancro AIRC (IG 17063); CMB is supported by FAR2017 (Unife).
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LM carry out bioinformatic analysis, FB performed the experiments on culture cell lines, MG revised the manuscript critically and suggested some idea to improve the work, NB conceived the study. SV and CMB participated in financing and experimental design. NB, CMB, LM and SV carried it out and drafted the manuscript. All authors approved the final manuscript.
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The research has been performed on commercially available cell lines and taken advantage of data sets store in public databanks not involving Human Participants and/or Animals.
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Suppl. Figure
1 Pattern of evolution divergence of LOC107987281 lncRNA. Cladogram from UCSC Genome Browser (http://genome.UCSC.edu). (TIFF 118 kb)
Suppl. Figure
2 Sequence alignment of LOC107987281 lncRNA. This track shows multiple alignments of 100 vertebrate species in UCSC Genome Browser (http://genome.UCSC.edu). (TIFF 799 kb)
Suppl. Figure
3 Sequence alignment of TGM2. This track shows multiple alignments of 100 vertebrate species in UCSC Genome Browser (http://genome.UCSC.edu). (TIFF 969 kb)
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Minotti, L., Baldassari, F., Galasso, M. et al. A long non-coding RNA inside the type 2 transglutaminase gene tightly correlates with the expression of its transcriptional variants. Amino Acids 50, 421–438 (2018). https://doi.org/10.1007/s00726-017-2528-9
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DOI: https://doi.org/10.1007/s00726-017-2528-9