m6A RNA Methylation Regulates the Self-Renewal and Tumorigenesis of Glioblastoma Stem Cells

Abstract

RNA modifications play critical roles in important biological processes. However, the functions of N 6 -methyladenosine (m 6 A) mRNA modification in cancer biology and cancer stem cells remain largely unknown. Here, we show that m 6 A mRNA modification is critical for glioblastoma stem cell (GSC) self-renewal and tumorigenesis. Knockdown of METTL3 or METTL14, key components of the RNA methyltransferase complex, dramatically promotes human GSC growth, self-renewal, and tumorigenesis. In contrast, overexpression of METTL3 or inhibition of the RNA demethylase FTO suppresses GSC growth and self-renewal. Moreover, inhibition of FTO suppresses tumor progression and prolongs lifespan of GSC-grafted mice substantially. m 6 A sequencing reveals that knockdown of METTL3 or METTL14 induced changes in mRNA m 6 A enrichment and altered mRNA expression of genes (e.g., ADAM19 ) with critical biological functions in GSCs. In summary, this study identifies the m 6 A mRNA methylation machinery as promising therapeutic targets for glioblastoma.

References 58

1. 1.

   Allegra A, Alonci A, Penna G, Innao V, Gerace D, Rotondo F, Musolino C. The cancer stem cell hypothesis: a guide to potential molecular targets. Cancer Invest. 2014;32:470-495.

   Not in our library10.3109/07357907.2014.958231

2. 2.

   Anido J, Sáez-Borderías A, Gonzàlez-Juncà A, Rodón L, Folch G, Carmona MA, Prieto-Sánchez RM, Barba I, Martínez-Sáez E, Prudkin L, et al. TGF-β receptor inhibitors target the CD44(high)/Id1(high) glioma-initiating cell population in human glioblastoma. Cancer Cell. 2010;18:655-668.

   Not in our library10.1016/j.ccr.2010.10.023

3. 3.

   Bao S, Wu Q, McLendon RE, Hao Y, Shi Q, Hjelmeland AB, Dewhirst MW, Bigner DD, Rich JN. Glioma stem cells promote radioresistance by preferential activation of the DNA damage response. Nature. 2006;444:756-760.

   Not in our library10.1038/nature05236

4. 4.

   Batista PJ, Molinie B, Wang J, Qu K, Zhang J, Li L, Bouley DM, Lujan E, Haddad B, Daneshvar K, et al. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell. 2014;15:707-719.

   Not in our library10.1016/j.stem.2014.09.019

5. 5.

   Bokar JA, Rath-Shambaugh ME, Ludwiczak R, Narayan P, Rottman F. Characterization and partial purification of mRNA N6-adenosine methyltransferase from HeLa cell nuclei. Internal mRNA methylation requires a multisubunit complex. J Biol Chem. 1994;269:17697-17704.

   Not in our library

6. 6.

   Bokar JA, Shambaugh ME, Polayes D, Matera AG, Rottman FM. Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. RNA. 1997;3:1233-1247.

   Not in our library

7. 7.

   Brown CE, Starr R, Martinez C, Aguilar B, D'Apuzzo M, Todorov I, Shih CC, Badie B, Hudecek M, Riddell SR, Jensen MC. Recognition and killing of brain tumor stem-like initiating cells by CD8+ cytolytic T cells. Cancer Res. 2009;69:8886-8893.

   Not in our library10.1158/0008-5472.can-09-2687

8. 8.

   Chen T, Hao YJ, Zhang Y, Li MM, Wang M, Han W, Wu Y, Lv Y, Hao J, Wang L, et al. m(6)A RNA methylation is regulated by micro-RNAs and promotes reprogramming to pluripotency. Cell Stem Cell. 2015;16:289-301.

   Not in our library10.1016/j.stem.2015.01.016

9. 9.

   Cui Q, Yang S, Ye P, Tian E, Sun G, Zhou J, Sun G, Liu X, Chen C, Murai K, et al. Downregulation of TLX induces TET3 expression and inhibits glioblastoma stem cell self-renewal and tumorigenesis. Nat Commun. 2016;7:10637.

   Not in our library10.1038/ncomms10637

10. 10.

    Desrosiers R, Friderici K, Rottman F. Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells. Proc Natl Acad Sci USA. 1974;71:3971-3975.

    Not in our library10.1073/pnas.71.10.3971

11. 11.

    Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, Cesarkas K, Jacob-Hirsch J, Amariglio N, Kupiec M, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012;485:201-206.

    Not in our library10.1038/nature11112

12. 12.

    Dominissini D, Moshitch-Moshkovitz S, Salmon-Divon M, Amariglio N, Rechavi G. Transcriptome-wide mapping of N(6)-methyladeno-sine by m(6)A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc. 2013;8:176-189.

    Not in our library10.1038/nprot.2012.148

13. 13.

    Dubin DT, Taylor RH. The methylation state of poly A-containing messenger RNA from cultured hamster cells. Nucleic Acids Res. 1975;2:1653-1668.

    Not in our library10.1093/nar/2.10.1653

14. 14.

    Fustin JM, Doi M, Yamaguchi Y, Hida H, Nishimura S, Yoshida M, Isagawa T, Morioka MS, Kakeya H, Manabe I, Okamura H. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell. 2013;155:793-806.

    Not in our library10.1016/j.cell.2013.10.026

15. 15.

    Geula S, Moshitch-Moshkovitz S, Dominissini D, Mansour AA, Kol N, Salmon-Divon M, Hershkovitz V, Peer E, Mor N, Manor YS, et al. m6A mRNA methylation facilitates resolution of naive pluripotency toward differentiation. Science. 2015;347:1002-1006.

    Not in our library10.1126/science.1261417

16. 16.

    Godlewski J, Newton HB, Chiocca EA, Lawler SE. MicroRNAs and glioblastoma; the stem cell connection. Cell Death Differ. 2010;17:221-228.

    Not in our library10.1038/cdd.2009.71

17. 17.

    Guruswamy S, Swamy MV, Choi CI, Steele VE, Rao CV. S-adenosyl L-methionine inhibits azoxymethane-induced colonic aberrant crypt foci in F344 rats and suppresses human colon cancer Caco-2 cell growth in 3D culture. Int J Cancer. 2008;122:25-30.

    Not in our library10.1002/ijc.23031

18. 18.

    Haussmann IU, Bodi Z, Sanchez-Moran E, Mongan NP, Archer N, Fray RG, Soller M. m(6)A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination. Nature. 2016;540:301-304.

    Not in our library10.1038/nature20577

19. 19.
    Meclofenamic acid selectively inhibits FTO demethylation of m6A over ALKBH5 · 2014

    No notice
20. 20.

    Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, Yi C, Lindahl T, Pan T, Yang YG, He C. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011;7:885-887.

    Not in our library10.1038/nchembio.687

21. 21.

    Johnson DR, O'Neill BP. Glioblastoma survival in the United States before and during the temozolomide era. J Neurooncol. 2012;107:359-364.

    Not in our library10.1007/s11060-011-0749-4

22. 22.
    The role of the fat mass and obesity associated gene (FTO) in breast cancer risk · 2011

    No notice
23. 23.

    Lang MF, Yang S, Zhao C, Sun G, Murai K, Wu X, Wang J, Gao H, Brown CE, Liu X, et al. Genome-wide profiling identified a set of miRNAs that are differentially expressed in glioblastoma stem cells and normal neural stem cells. PLoS ONE. 2012;7:e36248.

    Not in our library10.1371/journal.pone.0036248

24. 24.

    Lemkine GF, Raj A, Alfama G, Turque N, Hassani Z, Alegria-Prévot O, Samarut J, Levi G, Demeneix BA. Adult neural stem cell cycling in vivo requires thyroid hormone and its alpha receptor. FASEB J. 2005;19:863-865.

    Not in our library10.1096/fj.04-2916fje

25. 25.

    Lence T, Akhtar J, Bayer M, Schmid K, Spindler L, Ho CH, Kreim N, Andrad-Navarro MA, Poeck B, Helm M, Roignant JY. m6A medulates neuronal functions and sex determination in Drosophila. Nature. 2016;540:242-247.

    Not in our library10.1038/nature20568

26. 26.

    Li Z, Weng H, Su R, Weng X, Zuo Z, Li C, Huang H, Nachtergaele S, Dong L, Hu C, et al. FTO plays an oncogenic role in acute myeloid leukemia as a N(6)-methyladenosine RNA demethylase. Cancer Cell. 2017;31:127-141.

    Not in our library10.1016/j.ccell.2016.11.017

27. 27.

    Lin S, Choe J, Du P, Triboulet R, Gregory RI. The m(6)A methyltransferase METTL3 promotes translation in human cancer cells. Mol Cell. 2016;62:335-345.

    Not in our library10.1016/j.molcel.2016.03.021

28. 28.

    Linnebacher M, Wienck A, Boeck I, Klar E. Identification of an MSI-H tumor-specific cytotoxic T cell epitope generated by the (-1) frame of U79260(FTO). J Biomed Biotechnol. 2010;2010:841451.

    Not in our library10.1155/2010/841451

29. 29.

    Liu J, Yue Y, Han D, Wang X, Fu Y, Zhang L, Jia G, Yu M, Lu Z, Deng X, et al. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol. 2014;10:93-95.

    Not in our library10.1038/nchembio.1432

30. 30.

    Long J, Zhang B, Signorello LB, Cai Q, Deming-Halverson S, Shrubsole MJ, Sanderson M, Dennis J, Michailidou K, Easton DF, et al. Evaluating genome-wide association study-identified breast cancer risk variants in African-American women. PLoS ONE. 2013;8:e58350.

    Not in our library10.1371/journal.pone.0058350

31. 31.

    Lu SC, Ramani K, Ou X, Lin M, Yu V, Ko K, Park R, Bottiglieri T, Tsukamoto H, Kanel G, et al. S-adenosylmethionine in the chemoprevention and treatment of hepatocellular carcinoma in a rat model. Hepatology. 2009;50:462-471.

    Not in our library10.1002/hep.22990

32. 32.

    Machiela MJ, Lindström S, Allen NE, Haiman CA, Albanes D, Barricarte A, Berndt SI, Bueno-de-Mesquita HB, Chanock S, Gaziano JM, et al. Association of type 2 diabetes susceptibility variants with advanced prostate cancer risk in the Breast and Prostate Cancer Cohort Consortium. Am J Epidemiol. 2012;176:1121-1129.

    Not in our library10.1093/aje/kws191

33. 33.

    Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, Olchowik A, Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, et al. MODOMICS: a database of RNA modification pathways– 2013 update. Nucleic Acids Res. 2013;41:D262-D267.

    Not in our library10.1093/nar/gks1007

34. 34.

    Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell. 2012;149:1635-1646.

    Not in our library10.1016/j.cell.2012.05.003

35. 35.

    Mochizuki S, Okada Y. ADAMs in cancer cell proliferation and progression. Cancer Sci. 2007;98:621-628.

    Not in our library10.1111/j.1349-7006.2007.00434.x

36. 36.

    Pakneshan P, Szyf M, Farias-Eisner R, Rabbani SA. Reversal of the hypomethylation status of urokinase (uPA) promoter blocks breast cancer growth and metastasis. J Biol Chem. 2004;279:31735-31744.

    Not in our library10.1074/jbc.m401669200

37. 37.

    Pascale RM, Simile MM, De Miglio MR, Feo F. Chemoprevention of hepatocarcinogenesis: S-adenosyl-L-methionine. Alcohol. 2002;27:193-198.

    Not in our library10.1016/s0741-8329(02)00227-6

38. 38.

    Perry RP, Kelley DE, Friderici K, Rottman F. The methylated constituents of L cell messenger RNA: evidence for an unusual cluster at the 5′ terminus. Cell. 1975;4:387-394.

    Not in our library10.1016/0092-8674(75)90159-2

39. 39.

    Pierce BL, Austin MA, Ahsan H. Association study of type 2 diabetes genetic susceptibility variants and risk of pancreatic cancer: an analysis of PanScan-I data. Cancer Causes Control. 2011;22:877-883.

    Not in our library10.1007/s10552-011-9760-5

40. 40.

    Pietras A, Katz AM, Ekström EJ, Wee B, Halliday JJ, Pitter KL, Werbeck JL, Amankulor NM, Huse JT, Holland EC. Osteopontin-CD44 signaling in the glioma perivascular niche enhances cancer stem cell phenotypes and promotes aggressive tumor growth. Cell Stem Cell. 2014;14:357-369.

    Not in our library10.1016/j.stem.2014.01.005

41. 41.

    Ping XL, Sun BF, Wang L, Xiao W, Yang X, Wang WJ, Adhikari S, Shi Y, Lv Y, Chen YS, et al. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 2014;24:177-189.

    Not in our library10.1038/cr.2014.3

42. 42.

    Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, et al. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell. 2013;155:1409-1421.

    Not in our library10.1016/j.cell.2013.10.047

43. 43.

    Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, et al. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5′ sites. Cell Rep. 2014;8:284-296.

    Not in our library10.1016/j.celrep.2014.05.048

44. 44.

    Shi Y, Chichung Lie D, Taupin P, Nakashima K, Ray J, Yu RT, Gage FH, Evans RM. Expression and function of orphan nuclear receptor TLX in adult neural stem cells. Nature. 2004;427:78-83.

    Not in our library10.1038/nature02211

45. 45.

    Sibbritt T, Patel HR, Preiss T. Mapping and significance of the mRNA methylome. Wiley Interdiscip Rev RNA. 2013;4:397-422.

    Not in our library10.1002/wrna.1166

46. 46.

    Singh SK, Hawkins C, Clarke ID, Squire JA, Bayani J, Hide T, Henkelman RM, Cusimano MD, Dirks PB. Identification of human brain tumour initiating cells. Nature. 2004;432:396-401.

    Not in our library10.1038/nature03128

47. 47.

    Stupp R, Hegi ME, Mason WP, van den Bent MJ, Taphoorn MJ, Janzer RC, Ludwin SK, Allgeier A, Fisher B, Belanger K, et al. Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol. 2009;10:459-466.

    Not in our library10.1016/s1470-2045(09)70025-7

48. 48.

    Sundar SJ, Hsieh JK, Manjila S, Lathia JD, Sloan A. The role of cancer stem cells in glioblastoma. Neurosurg Focus. 2014;37:E6.

    Not in our library10.3171/2014.9.focus14494

49. 49.

    Wang Y, Li Y, Toth JI, Petroski MD, Zhang Z, Zhao JC. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat Cell Biol. 2014;16:191-198.

    Not in our library10.1038/ncb2902

50. 50.

    Wei CM, Moss B. Methylation of newly synthesized viral messenger RNA by an enzyme in vaccinia virus. Proc Natl Acad Sci USA. 1974;71:3014-3018.

    Not in our library10.1073/pnas.71.8.3014

51. 51.

    Wei CM, Gershowitz A, Moss B. Methylated nucleotides block 5′ terminus of HeLa cell messenger RNA. Cell. 1975;4:379-386.

    Not in our library10.1016/0092-8674(75)90158-0

52. 52.

    Wildeboer D, Naus S, Amy Sang QX, Bartsch JW, Pagenstecher A. Metalloproteinase disintegrins ADAM8 and ADAM19 are highly regulated in human primary brain tumors and their expression levels and activities are associated with invasiveness. J Neuropathol Exp Neurol. 2006;65:516-527.

    Not in our library10.1097/01.jnen.0000229240.51490.d3

53. 53.

    Yue Y, Liu J, He C. RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev. 2015;29:1343-1355.

    Not in our library10.1101/gad.262766.115

54. 54.

    Zhang C, Samanta D, Lu H, Bullen JW, Zhang H, Chen I, He X, Semenza GL. Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA. Proc Natl Acad Sci USA. 2016;113:E2047-E2056.

    Not in our library10.1073/pnas.1602883113

55. 55.

    Zhao Y, Li JS, Guo MZ, Feng BS, Zhang JP. Inhibitory effect of S-adenosylmethionine on the growth of human gastric cancer cells in vivo and in vitro. Chin J Cancer. 2010;29:752-760.

    Not in our library10.5732/cjc.010.10046

56. 56.

    Zhao X, Yang Y, Sun BF, Shi Y, Yang X, Xiao W, Hao YJ, Ping XL, Chen YS, Wang WJ, et al. FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res. 2014;24:1403-1419.

    Not in our library10.1038/cr.2014.151

57. 57.

    Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, Vågbø CB, Shi Y, Wang WL, Song SH, et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell. 2013;49:18-29.

    Not in our library10.1016/j.molcel.2012.10.015

58. 58.

    Zhou J, Wan J, Gao X, Zhang X, Jaffrey SR, Qian SB. Dynamic m(6)A mRNA methylation directs translational control of heat shock response. Nature. 2015;526:591-594.

    Not in our library10.1038/nature15377

Cited by papers we hold 81

• Cancer epigenetics: from laboratory studies and clinical trials to precision medicine · 2024
  No notice
• RNA modification: mechanisms and therapeutic targets · 2023
  No notice
• The Potential Role of m6A RNA Methylation in the Aging Process and Aging-Associated Diseases · 2022
  Not checked
• m6A modification: recent advances, anticancer targeted drug discovery and beyond · 2022
  No notice
• FTO m6A Demethylase in Obesity and Cancer: Implications and Underlying Molecular Mechanisms · 2022
  No notice
• The RNA m6A writer WTAP in diseases: structure, roles, and mechanisms · 2022
  No notice
• Functions, mechanisms, and therapeutic implications of METTL14 in human cancer · 2022
  No notice
• Targeting the RNA m6A modification for cancer immunotherapy · 2022
  No notice
• Role of main RNA modifications in cancer: N6-methyladenosine, 5-methylcytosine, and pseudouridine · 2022
  No notice
• METTL3 Promotes Esophageal Squamous Cell Carcinoma Metastasis Through Enhancing GLS2 Expression · 2021
  Not checked
• FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell · 2021
  No notice
• N6-Methyladenosine Methyltransferase METTL14-Mediated Autophagy in Malignant Development of Oral Squamous Cell Carcinoma · 2021
  Not checked
• ADAR1 is a new target of METTL3 and plays a pro-oncogenic role in glioblastoma by an editing-independent mechanism · 2021
  No notice
• Recent advances of m6A methylation modification in esophageal squamous cell carcinoma · 2021
  Not checked
• Autophagy of the m6A mRNA demethylase FTO is impaired by low-level arsenic exposure to promote tumorigenesis · 2021
  No notice
• Identification of IGF2BP3 as an Adverse Prognostic Biomarker of Gliomas · 2021
  Not checked
• The RNA N6-Methyladenosine Methyltransferase METTL3 Promotes the Progression of Kidney Cancer via N6-Methyladenosine-Dependent Translational Enhancement of ABCD1 · 2021
  Not checked
• EGFR/SRC/ERK-stabilized YTHDF2 promotes cholesterol dysregulation and invasive growth of glioblastoma · 2021
  No notice
• The role of m6A modification in the biological functions and diseases · 2021
  No notice
• YTHDF2 facilitates UBXN1 mRNA decay by recognizing METTL3-mediated m6A modification to activate NF-κB and promote the malignant progression of glioma · 2021
  No notice

and 61 more

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.