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Research Article

Integrated Analysis of Transcriptome-Wide m6A Methylome of Osteosarcoma Stem Cells Enriched by Chemotherapy

, , , , , , , & show all
Pages 1693-1715 | Received 09 Sep 2019, Accepted 07 Oct 2019, Published online: 25 Oct 2019

References

  • Gianferante DM , MirabelloL , SavageSA. Germline and somatic genetics of osteosarcoma - connecting aetiology, biology and therapy. Nat. Rev. Endocrinol.13(8), 480–491 (2017).
  • Siclari VA , QinL. Targeting the osteosarcoma cancer stem cell. J. Orthop. Surg. Res.5, 78 (2010).
  • Isakoff MS , BielackSS , MeltzerP , GorlickR. Osteosarcoma: current treatment and a collaborative pathway to success. J. Clin. Oncol.33(27), 3029–3035 (2015).
  • Kansara M , TengMW , SmythMJ , ThomasDM. Translational biology of osteosarcoma. Nat. Rev. Cancer14(11), 722–735 (2014).
  • Brown HK , Tellez-GabrielM , HeymannD. Cancer stem cells in osteosarcoma. Cancer Lett.386, 189–195 (2017).
  • Yan GN , LvYF , GuoQN. Advances in osteosarcoma stem cell research and opportunities for novel therapeutic targets. Cancer Lett.370(2), 268–274 (2016).
  • Martins-Neves SR , Paiva-OliveiraDI , Wijers-KosterPMet al. Chemotherapy induces stemness in osteosarcoma cells through activation of Wnt/beta-catenin signaling. Cancer Lett.370(2), 286–295 (2016).
  • Yu L , FanZ , FangSet al. Cisplatin selects for stem-like cells in osteosarcoma by activating Notch signaling. Oncotarget7(22), 33055–33068 (2016).
  • Tang QL , LiangY , XieXBet al. Enrichment of osteosarcoma stem cells by chemotherapy. Chin. J. Cancer30(6), 426–432 (2011).
  • Wei CM , GershowitzA , MossB. Methylated nucleotides block 5′ terminus of HeLa cell messenger RNA. Cell4(4), 379–386 (1975).
  • Zhao BS , HeC. Fate by RNA methylation: m6A steers stem cell pluripotency. Genome Biol.16, 43 (2015).
  • Geula S , Moshitch-MoshkovitzS , DominissiniDet al. Stem cells. m6A mRNA methylation facilitates resolution of naive pluripotency toward differentiation. Science347(6225), 1002–1006 (2015).
  • Zhang C , ChenY , SunBet al. m(6)A modulates haematopoietic stem and progenitor cell specification. Nature549(7671), 273–276 (2017).
  • Vu LP , PickeringBF , ChengYet al. The N(6)-methyladenosine (m(6)A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. Nat. Med.23(11), 1369–1376 (2017).
  • Barbieri I , TzelepisK , PandolfiniLet al. Promoter-bound METTL3 maintains myeloid leukaemia by m(6)A-dependent translation control. Nature552(7683), 126–131 (2017).
  • Weng H , HuangH , WuHet al. METTL14 inhibits hematopoietic stem/progenitor differentiation and promotes leukemogenesis via mRNA m(6)A modification. Cell Stem Cell22(2), 191–205.e199 (2018).
  • Cui Q , ShiH , YePet al. m(6)A RNA methylation regulates the self-renewal and tumorigenesis of glioblastoma stem cells. Cell Rep.18(11), 2622–2634 (2017).
  • Zhang S , ZhaoBS , ZhouAet al. m(6)A demethylase ALKBH5 maintains tumorigenicity of glioblastoma stem-like cells by sustaining FOXM1 expression and cell proliferation program. Cancer Cell31(4), 591–606.e596 (2017).
  • Meyer KD , SaletoreY , ZumboP , ElementoO , MasonCE , JaffreySR. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell149(7), 1635–1646 (2012).
  • Dominissini D , Moshitch-MoshkovitzS , SchwartzSet al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature485(7397), 201–206 (2012).
  • Luo GZ , MacqueenA , ZhengGet al. Unique features of the m6A methylome in Arabidopsis thaliana. Nat. Commun.5, 5630 (2014).
  • Oda Y , MatsumotoY , HarimayaK , IwamotoY , TsuneyoshiM. Establishment of new multidrug-resistant human osteosarcoma cell lines. Oncol. Rep.7(4), 859–866 (2000).
  • Han XG , DuL , QiaoHet al. CXCR1 knockdown improves the sensitivity of osteosarcoma to cisplatin. Cancer Lett.369(2), 405–415 (2015).
  • Tirino V , DesiderioV , PainoF , PapaccioG , DeRosa M. Methods for cancer stem cell detection and isolation. Methods Mol. Biol.879, 513–529 (2012).
  • Zhang Y , LiuT , MeyerCAet al. Model-based analysis of ChIP-Seq (MACS). Genome Biol.9(9), R137 (2008).
  • Heinz S , BennerC , SpannNet al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell38(4), 576–589 (2010).
  • Olarerin-George AO , JaffreySR. MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites. Bioinformatics33(10), 1563–1564 (2017).
  • Shen L , ShaoNY , LiuX , MazeI , FengJ , NestlerEJ. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS ONE8(6), e65598 (2013).
  • Chen Y , ChenY , ShiCet al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience7(1), 1–6 (2018).
  • Langmead B , SalzbergSL. Fast gapped-read alignment with Bowtie 2. Nat. Methods9(4), 357–359 (2012).
  • Li B , DeweyCN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics12, 323 (2011).
  • Wang L , FengZ , WangX , WangX , ZhangX. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics26(1), 136–138 (2010).
  • Edgar R , DomrachevM , LashAE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res.30(1), 207–210 (2002).
  • Rainusso N , ManTK , LauCCet al. Identification and gene expression profiling of tumor-initiating cells isolated from human osteosarcoma cell lines in an orthotopic mouse model. Cancer Biol. Ther.12(4), 278–287 (2011).
  • Tirino V , DesiderioV , D’aquinoRet al. Detection and characterization of CD133+ cancer stem cells in human solid tumours. PLoS ONE3(10), e3469 (2008).
  • Adhikari AS , AgarwalN , WoodBMet al. CD117 and Stro-1 identify osteosarcoma tumor-initiating cells associated with metastasis and drug resistance. Cancer Res.70(11), 4602–4612 (2010).
  • Chou AJ , GorlickR. Chemotherapy resistance in osteosarcoma: current challenges and future directions. Expert. Rev. Anticancer Ther.6(7), 1075–1085 (2006).
  • Marina NM , SmelandS , BielackSSet al. Comparison of MAPIE versus MAP in patients with a poor response to preoperative chemotherapy for newly diagnosed high-grade osteosarcoma (EURAMOS-1): an open-label, international, randomised controlled trial. Lancet Oncol.17(10), 1396–1408 (2016).
  • Suva ML , RheinbayE , GillespieSMet al. Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell157(3), 580–594 (2014).
  • Mani SA , GuoW , LiaoMJet al. The epithelial-mesenchymal transition generates cells with properties of stem cells. Cell133(4), 704–715 (2008).
  • Liu X , KrawczykE , SuprynowiczFAet al. Conditional reprogramming and long-term expansion of normal and tumor cells from human biospecimens. Nat. Protoc.12(2), 439–451 (2017).
  • Saenz FR , OryV , AlotaibyMet al. Conditionally reprogrammed normal and transformed mouse mammary epithelial cells display a progenitor-cell-like phenotype. PLoS ONE9(5), e97666 (2014).
  • Wang P , WanWW , XiongSL , FengH , WuN. Cancer stem-like cells can be induced through dedifferentiation under hypoxic conditions in glioma, hepatoma and lung cancer. Cell Death Discov.3, 16105 (2017).
  • Wan ACA . Primitive cancer cell states: a target for drug screening?Trends Pharmacol. Sci.40(3), 161–171 (2019).
  • Wang Y , MaoJ , WangXet al. Genome-wide screening of altered m6A-tagged transcript profiles in the hippocampus after traumatic brain injury in mice. Epigenomics11(7), 805–819 (2019).
  • Luo Z , ZhangZ , TaiL , ZhangL , SunZ , ZhouL. Comprehensive analysis of differences of N(6)-methyladenosine RNA methylomes between high-fat-fed and normal mouse livers. Epigenomics11(11), 1267–1282 (2019).
  • Zhou J , WanJ , GaoX , ZhangX , JaffreySR , QianSB. Dynamic m(6)A mRNA methylation directs translational control of heat shock response. Nature526(7574), 591–594 (2015).
  • Fry NJ , LawBA , IlkayevaOR , HolleyCL , MansfieldKD. N(6)-methyladenosine is required for the hypoxic stabilization of specific mRNAs. Rna23(9), 1444–1455 (2017).
  • Anders M , ChelyshevaI , GoebelIet al. Dynamic m(6)A methylation facilitates mRNA triaging to stress granules. Life Sci. Alliance1(4), e201800113 (2018).
  • Kun-Peng Z , Xiao-LongM , LeiZ , Chun-LinZ , Jian-PingH , Tai-ChengZ. Screening circular RNA related to chemotherapeutic resistance in osteosarcoma by RNA sequencing. Epigenomics10(10), 1327–1346 (2018).
  • Liu T , LiZ , ZhangQet al. Targeting ABCB1 (MDR1) in multi-drug resistant osteosarcoma cells using the CRISPR-Cas9 system to reverse drug resistance. Oncotarget7(50), 83502–83513 (2016).
  • Li S , SunW , WangH , ZuoD , HuaY , CaiZ. Research progress on the multidrug resistance mechanisms of osteosarcoma chemotherapy and reversal. Tumour Biol.36(3), 1329–1338 (2015).
  • Lin S , ChoeJ , DuP , TribouletR , GregoryRI. The m(6)A methyltransferase METTL3 promotes translation in human cancer cells. Mol. Cell62(3), 335–345 (2016).
  • Miao W , ChenJ , JiaL , MaJ , SongD. The m6A methyltransferase METTL3 promotes osteosarcoma progression by regulating the m6A level of LEF1. Biochem. Biophys. Res. Commun.516(3), 719–725 (2019).
  • Ma JZ , YangF , ZhouCCet al. METTL14 suppresses the metastatic potential of hepatocellular carcinoma by modulating N(6) -methyladenosine-dependent primary MicroRNA processing. Hepatology65(2), 529–543 (2017).
  • Zhang C , SamantaD , LuHet al. Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m(6)A-demethylation of NANOG mRNA. Proc. Natl Acad. Sci. USA113(14), E2047–E2056 (2016).
  • Qi XT , LiYL , ZhangYQet al. KLF4 functions as an oncogene in promoting cancer stem cell-like characteristics in osteosarcoma cells. Acta Pharmacol. Sin.40(4), 546–555 (2019).
  • Martins-Neves SR , CorverWE , Paiva-OliveiraDIet al. Osteosarcoma stem cells have active Wnt/beta-catenin and overexpress SOX2 and KLF4. J. Cell. Physiol.231(4), 876–886 (2016).
  • Wang J , PangW , ZuoZ , ZhangW , HeW. MicroRNA-520b suppresses proliferation, migration, and invasion of spinal osteosarcoma cells via downregulation of Frizzled-8. Oncol. Res.25(8), 1297–1304 (2017).
  • Wakefield LM , HillCS. Beyond TGFbeta: roles of other TGFbeta superfamily members in cancer. Nat. Rev. Cancer13(5), 328–341 (2013).
  • Kielman MF , RindapaaM , GasparCet al. Apc modulates embryonic stem-cell differentiation by controlling the dosage of beta-catenin signaling. Nat. Genet.32(4), 594–605 (2002).
  • Cheng Y , CheungAK , KoJMet al. Physiological beta-catenin signaling controls self-renewal networks and generation of stem-like cells from nasopharyngeal carcinoma. BMC Cell Biol.14, 44 (2013).
  • Sato N , MeijerL , SkaltsounisL , GreengardP , BrivanlouAH. Maintenance of pluripotency in human and mouse embryonic stem cells through activation of Wnt signaling by a pharmacological GSK-3-specific inhibitor. Nat. Med.10(1), 55–63 (2004).
  • Ten Berge D , KurekD , BlauwkampTet al. Embryonic stem cells require Wnt proteins to prevent differentiation to epiblast stem cells. Nat. Cell Biol.13(9), 1070–1075 (2011).
  • Wang L , ParkP , ZhangHet al. BMP-2 inhibits the tumorigenicity of cancer stem cells in human osteosarcoma OS99-1 cell line. Cancer Biol. Ther.11(5), 457–463 (2011).
  • Geng S , SunB , LuR , WangJ. Coleusin factor, a novel anticancer diterpenoid, inhibits osteosarcoma growth by inducing bone morphogenetic protein-2-dependent differentiation. Mol. Cancer Ther.13(6), 1431–1441 (2014).
  • Zhang H , WuH , ZhengJet al. Transforming growth factor beta1 signal is crucial for dedifferentiation of cancer cells to cancer stem cells in osteosarcoma. Stem Cells31(3), 433–446 (2013).
  • He A , QiW , HuangYet al. CD133 expression predicts lung metastasis and poor prognosis in osteosarcoma patients: a clinical and experimental study. Exp. Ther. Med.4(3), 435–441 (2012).