FTO-mediated m⁶A demethylation regulates IGFBP3 expression and AKT activation through IMP3-dependent P-body re-localisation in lung cancer

Abstract

Lung cancer remains one of the leading causes of cancer-related deaths worldwide, and a growing body of evidence suggests that RNA modifications, including methylation, play a critical role in its progression. In this study, we investigated the role of the RNA demethylase fat mass and obesity-associated protein (FTO) in lung cancer progression and determined the underlying molecular mechanisms. FTO expression was significantly upregulated in LUAD and correlated with poor prognosis. FTO knockdown in lung patient-derived organoids and LUAD cell lines reduced their proliferation, invasion, and migration, and FTO knockdown in a Kras^G12D mouse model reduced the growth of lung tumours. Mechanistically, FTO demethylated m⁶A sites in the insulin-like growth factor-binding protein 3 (IGFBP3) 3′UTR, preventing IMP3 binding. The ribonuclear protein IMP3 was identified as a crucial functional reader that interacted with m⁶A-modified sites in the IGFBP3 3′UTR, thereby promoting IGFBP3 mRNA localisation to P-bodies and suppressing its translation. Elevated IGFBP3 activated AKT signalling and promoted tumour progression. Collectively, we revealed that FTO drives lung cancer progression via m⁶A-dependent sequestration of IGFBP3 mRNA into P-bodies by IMP3, which suppresses translation and activates AKT signalling. The FTO–IGFBP3–AKT axis thus represents a promising therapeutic target.

Keywords

FTO / IGFBP3 / lung adenocarcinoma / m⁶A / P-bodies

References

[1] Coudray N, Ocampo PS, Sakellaropoulos T, et al. Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning. Nat Med. 2018; 24: 1559-1567.

[2] Kuncman Ł, Orzechowska M, Milecki T, Kucharz J, Fijuth J. High FLT3 expression increases immune-cell infiltration in the tumor microenvironment and correlates with prolonged disease-free survival in patients with non-small cell lung cancer. Mol Oncol. 2024; 18: 1316-1326.

[3] Li Y, Su R, Deng X, Chen Y, Chen J. FTO in cancer: functions, molecular mechanisms, and therapeutic implications. Trends Cancer. 2022; 8: 598-614.

[4] Chen XY, Zhang J, Zhu JS. The role of m(6)A RNA methylation in human cancer. Mol Cancer. 2019; 18: 103.

[5] Su R, Dong L, Li Y, et al. Targeting FTO suppresses cancer stem cell maintenance and immune evasion. Cancer Cell. 2020; 38: 79-96.e11.

[6] Wei J, Liu F, Lu Z, et al. Differential m(6)A, m(6)A(m), and m(1)A demethylation mediated by FTO in the cell nucleus and cytoplasm. Mol Cell. 2018; 71: 973-985.e975.

[7] Zuidhof HR, Calkhoven CF. Oncogenic and tumor-suppressive functions of the RNA demethylase FTO. Cancer Res. 2022; 82: 2201-2212.

[8] Huang Y, Su R, Sheng Y, et al. Small-molecule targeting of oncogenic FTO demethylase in acute myeloid leukemia. Cancer Cell. 2019; 35: 677-691.e610.

[9] Cui Q, Shi H, Ye P, et al. m(6)A rna methylation regulates the self-renewal and tumorigenesis of glioblastoma stem cells. Cell Rep. 2017; 18: 2622-2634.

[10] Zhang J, Wei J, Sun R, et al. A lncRNA from the FTO locus acts as a suppressor of the m(6)A writer complex and p53 tumor suppression signaling. Mol Cell. 2023; 83: 2692-2708.e2697.

[11] Xu Y, Zhou J, Li L, et al. FTO-mediated autophagy promotes progression of clear cell renal cell carcinoma via regulating SIK2 mRNA stability. Int J Biol Sci. 2022; 18: 5943-5962.

[12] Xu Y, Ye S, Zhang N, et al. The FTO/miR-181b-3p/ARL5B signaling pathway regulates cell migration and invasion in breast cancer. Cancer Commun (Lond). 2020; 40: 484-500.

[13] Lin K, Zhou E, Shi T, et al. m⁶A eraser FTO impairs gemcitabine resistance in pancreatic cancer through influencing NEDD4 mRNA stability by regulating the PTEN/PI3K/AKT pathway. J Exp Clin Cancer Res. 2023; 42: 217.

[14] An Y, Duan H. The role of m⁶A RNA methylation in cancer metabolism. Mol Cancer. 2022; 21: 14.

[15] Ma S, Chen C, Ji X, et al. The interplay between m⁶A RNA methylation and noncoding RNA in cancer. J Hematol Oncol. 2019; 12: 121.

[16] Zhuang H, Yu B, Tao D, et al. The role of m⁶A methylation in therapy resistance in cancer. Mol Cancer. 2023; 22: 91.

[17] Huang J, Sun W, Wang Z, et al. FTO suppresses glycolysis and growth of papillary thyroid cancer via decreasing stability of APOE mRNA in an N6-methyladenosine-dependent manner. J Exp Clin Cancer Res. 2022; 41: 42.

[18] Ma L, Xue X, Zhang X, et al. The essential roles of m(6)A RNA modification to stimulate ENO1-dependent glycolysis and tumorigenesis in lung adenocarcinoma. J Exp Clin Cancer Res. 2022; 41: 36.

[19] Tan Z, Shi S, Xu J, et al. RNA N6-methyladenosine demethylase FTO promotes pancreatic cancer progression by inducing the autocrine activity of PDGFC in an m(6)A-YTHDF2-dependent manner. Oncogene. 2022; 41: 2860-2872.

[20] Jia G, Fu Y, Zhao X, et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011; 7: 885-887.

[21] Mauer J, Luo X, Blanjoie A, et al. Reversible methylation of m(6)A(m) in the 5' cap controls mRNA stability. Nature. 2017; 541: 371-375.

[22] Liu Y, Dong JH, Shen XY, et al. Qualitative and quantitative analytical techniques of nucleic acid modification based on mass spectrometry for biomarker discovery. Int J Mol Sci. 2024; 25(6): 3383.

[23] Zeng C, Huang W, Li Y, Weng H. Roles of METTL3 in cancer: mechanisms and therapeutic targeting. J Hematol Oncol. 2020; 13: 117.

[24] Shan M, Liu D, Sun L, et al. KIAA1429 facilitates metastasis via m⁶A-YTHDC1-dependent RND3 down-regulation in hepatocellular carcinoma cells. Cancer Lett. 2024; 584: 216598.

[25] Dasgupta P, Rizwani W, Pillai S, et al. ARRB1-mediated regulation of E2F target genes in nicotine-induced growth of lung tumors. J Natl Cancer Inst. 2011; 103: 317-333.

[26] Jin Z, Lu Y, Wu X, et al. The cross-talk between tumor cells and activated fibroblasts mediated by lactate/BDNF/TrkB signaling promotes acquired resistance to anlotinib in human gastric cancer. Redox Biol. 2021; 46: 102076.

[27] Tu W, Yang B, Leng X, et al. Testis-specific protein, Y-linked 1 activates PI3K/AKT and RAS signaling pathways through suppressing IGFBP3 expression during tumor progression. Cancer Sci. 2019; 110: 1573-1586.

[28] Zhao X, Mai Z, Liu L, Lu Y, Cui L, Yu J. Hypoxia-driven TNS4 fosters HNSCC tumorigenesis by stabilizing integrin α5β1 complex and triggering FAK-mediated Akt and TGFβ signaling pathways. Int J Biol Sci. 2024; 20: 231-248.

[29] Robinson JT, Thorvaldsdóttir H, Winckler W, et al. Integrative genomics viewer. Nat Biotechnol. 2011; 29: 24-26.

[30] Boissel S, Reish O, Proulx K, et al. Loss-of-function mutation in the dioxygenase-encoding FTO gene causes severe growth retardation and multiple malformations. Am J Hum Genet. 2009; 85: 106-111.

[31] Zheng Y, Nie P, Peng D, et al. m⁶AVar: a database of functional variants involved in m⁶A modification. Nucleic Acids Res. 2018; 46: D139-D145.

[32] Zhou Y, Zeng P, Li YH, Zhang Z, Cui Q. SRAMP: prediction of mammalian N6-methyladenosine (m⁶A) sites based on sequence-derived features. Nucleic Acids Res. 2016; 44: e91.

[33] Arab JP, Cabrera D, Sehrawat TS, et al. Hepatic stellate cell activation promotes alcohol-induced steatohepatitis through Igfbp3 and SerpinA12. J Hepatol. 2020; 73: 149-160.

[34] Li M, Wu W, Deng S, Shao Z, Jin X. TRAIP modulates the IGFBP3/AKT pathway to enhance the invasion and proliferation of osteosarcoma by promoting KANK1 degradation. Cell Death Dis. 2021; 12: 767.

[35] Li X, Zhang CC, Lin XT, et al. Elevated expression of WSB2 degrades p53 and activates the IGFBP3-AKT-mTOR-dependent pathway to drive hepatocellular carcinoma. Exp Mol Med. 2024; 56: 177-191.

[36] Ferrari U, Schmidmaier R, Jung T, et al. IGF-I/IGFBP3/ALS deficiency in sarcopenia: low GHBP suggests GH resistance in a subgroup of geriatric patients. J Clin Endocrinol Metab. 2021; 106: e1698-e1707.

[37] Upners EN, Ljubicic ML, Busch AS, et al. Dynamic changes in serum IGF-I and growth during infancy: associations to body fat, target height, and PAPPA2 genotype. J Clin Endocrinol Metab. 2022; 107: 219-229.

[38] Han G, Sinjab A, Rahal Z, et al. An atlas of epithelial cell states and plasticity in lung adenocarcinoma. Nature. 2024; 627: 656-663.

[39] Zhang L, Zhang Y, Wang C, et al. Integrated single-cell RNA sequencing analysis reveals distinct cellular and transcriptional modules associated with survival in lung cancer. Signal Transduct Target Ther. 2022; 7: 9.

[40] Lee JH, Wang R, Xiong F, et al. Enhancer RNA m⁶A methylation facilitates transcriptional condensate formation and gene activation. Mol Cell. 2021; 81: 3368-3385.e3369.

[41] Liu T, Wei Q, Jin J, et al. The m⁶A reader YTHDF1 promotes ovarian cancer progression via augmenting EIF3C translation. Nucleic Acids Res. 2020; 48: 3816-3831.

[42] Rauch S, He C, Dickinson BC. Targeted m(6)A reader proteins to study epitranscriptomic regulation of single RNAs. J Am Chem Soc. 2018; 140: 11974-11981.

[43] Xiong J, He J, Zhu J, et al. Lactylation-driven METTL3-mediated RNA m(6)A modification promotes immunosuppression of tumor-infiltrating myeloid cells. Mol Cell. 2022; 82: 1660-1677.e1610.

[44] Wang A, Huang H, Shi JH, et al. USP47 inhibits m⁶A-dependent c-Myc translation to maintain regulatory T cell metabolic and functional homeostasis. J Clin Invest. 2023; 133(23): e169365.

[45] Wu O, Jin Y, Zhang Z, et al. KMT2A regulates the autophagy-GATA4 axis through METTL3-mediated m(6)A modification of ATG4a to promote NPCs senescence and IVDD progression. Bone Res. 2024; 12: 67.

[46] Hsu PJ, Zhu Y, Ma H, et al. Ythdc2 is an N(6)-methyladenosine binding protein that regulates mammalian spermatogenesis. Cell Res. 2017; 27: 1115-1127.

[47] Brothers WR, Fakim H, Kajjo S, Fabian MR. P-bodies directly regulate MARF1-mediated mRNA decay in human cells. Nucleic Acids Res. 2022; 50: 7623-7636.

[48] Shan T, Liu F, Wen M, et al. m(6)A modification negatively regulates translation by switching mRNA from polysome to P-body via IGF2BP3. Mol Cell. 2023; 83: 4494-4508.e4496.

[49] Ozgur S, Chekulaeva M, Stoecklin G. Human Pat1b connects deadenylation with mRNA decapping and controls the assembly of processing bodies. Mol Cell Biol. 2010; 30: 4308-4323.

[50] Li Y, Chen R, Zhou Q, et al. LSm14A is a processing body-associated sensor of viral nucleic acids that initiates cellular antiviral response in the early phase of viral infection. Proc Natl Acad Sci U S A. 2012; 109: 11770-11775.

[51] Hubstenberger A, Courel M, Bénard M, et al. P-Body purification reveals the condensation of repressed mRNA regulons. Mol Cell. 2017; 68: 144-157.e145.

[52] Delaunay S, Frye M. RNA modifications regulating cell fate in cancer. Nat Cell Biol. 2019; 21: 552-559.

[53] Covelo-Molares H, Bartosovic M, Vanacova S. RNA methylation in nuclear pre-mRNA processing. Wiley Interdiscip Rev RNA. 2018; 9: e1489.

[54] Wang X, Lu Z, Gomez A, et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014; 505: 117-120.

[55] Wang X, Zhao BS, Roundtree IA, et al. N(6)-methyladenosine modulates messenger RNA translation efficiency. Cell. 2015; 161: 1388-1399.

[56] Zhao X, Yang Y, Sun BF, et al. FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res. 2014; 24: 1403-1419.

[57] Li Z, Weng H, Su R, et al. FTO plays an oncogenic role in acute myeloid leukemia as a N(6)-methyladenosine RNA demethylase. Cancer Cell. 2017; 31: 127-141.

[58] Zhou S, Bai ZL, Xia D, et al. FTO regulates the chemo-radiotherapy resistance of cervical squamous cell carcinoma (CSCC) by targeting β-catenin through mRNA demethylation. Mol Carcinog. 2018; 57: 590-597.

[59] Liu N, Dai Q, Zheng G, He C, Parisien M, Pan T. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature. 2015; 518: 560-564.

[60] Su R, Dong L, Li C, et al. R-2HG exhibits anti-tumor activity by targeting FTO/m(6)A/MYC/CEBPA signaling. Cell. 2018; 172: 90-105.e123.

[61] Zhang S, Zhao BS, Zhou A, et al. m(6)A demethylase ALKBH5 maintains tumorigenicity of glioblastoma stem-like cells by sustaining FOXM1 expression and cell proliferation program. Cancer Cell. 2017; 31: 591-606.e596.

[62] Wang X, Wu R, Liu Y, et al. m(6)A mRNA methylation controls autophagy and adipogenesis by targeting Atg5 and Atg7. Autophagy. 2020; 16: 1221-1235.

[63] Wang Q, Xie H, Peng H, Yan J, Han L, Ye G. ZC3H13 inhibits the progression of hepatocellular carcinoma through m(6)A-PKM2-Mediated glycolysis and enhances chemosensitivity. J Oncol. 2021; 2021: 1328444.

[64] Cao X, Geng Q, Fan D, et al. m(6)A methylation: a process reshaping the tumour immune microenvironment and regulating immune evasion. Mol Cancer. 2023; 22: 42.

[65] Deng F, Zhou R, Lin C, et al. Tumor-secreted dickkopf2 accelerates aerobic glycolysis and promotes angiogenesis in colorectal cancer. Theranostics. 2019; 9: 1001-1014.

[66] Niu Y, Lin Z, Wan A, et al. RNA N6-methyladenosine demethylase FTO promotes breast tumor progression through inhibiting BNIP3. Mol Cancer. 2019; 18: 46.

[67] Ng CS, Kasumba DM, Fujita T, Luo H. Spatio-temporal characterization of the antiviral activity of the XRN1-DCP1/2 aggregation against cytoplasmic RNA viruses to prevent cell death. Cell Death Differ. 2020; 27: 2363-2382.

[68] Brandmann T, Fakim H, Padamsi Z, et al. Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes. Embo J. 2018; 37(7): e97869.

[69] Cialek CA, Galindo G, Morisaki T, Zhao N, Montgomery TA, Stasevich TJ. Imaging translational control by Argonaute with single-molecule resolution in live cells. Nat Commun. 2022; 13: 3345.

[70] Ford L, Ling E, Kandel ER, Fioriti L. CPEB3 inhibits translation of mRNA targets by localizing them to P bodies. Proc Natl Acad Sci U S A. 2019; 116: 18078-18087.

[71] Messaggi-Sartor M, Marco E, Martínez-Téllez E, et al. Combined aerobic exercise and high-intensity respiratory muscle training in patients surgically treated for non-small cell lung cancer: a pilot randomized clinical trial. Eur J Phys Rehabil Med. 2019; 55: 113-122.

[72] Miyamoto S, Yano K, Sugimoto S, et al. Matrix metalloproteinase-7 facilitates insulin-like growth factor bioavailability through its proteinase activity on insulin-like growth factor binding protein 3. Cancer Res. 2004; 64: 665-671.

[73] Perks CM, Burrows C, Holly JM. Intrinsic, pro-apoptotic effects of IGFBP-3 on breast cancer cells are reversible: involvement of PKA, Rho, and ceramide. Front Endocrinol (Lausanne). 2011; 2: 13.

[74] Qiu N, He YF, Zhang SM, et al. Cullin7 enhances resistance to trastuzumab therapy in Her2 positive breast cancer via degrading IRS-1 and downregulating IGFBP-3 to activate the PI3K/AKT pathway. Cancer Lett. 2019; 464: 25-36.

[75] Hales EC, Taub JW, Matherly LH. New insights into Notch1 regulation of the PI3K-AKT-mTOR1 signaling axis: targeted therapy of γ-secretase inhibitor resistant T-cell acute lymphoblastic leukemia. Cell Signal. 2014; 26: 149-161.

[76] Tian S, Yu H, Yang R, Wang H, Zhao B, Wang D. IGFBP3 enhances adipose-derived stem cell function in soft tissue injury repair via ITGB1 and ERK pathway activation. Cell Biol Toxicol. 2025; 41: 85.

[77] Johnson L, Mercer K, Greenbaum D, et al. Somatic activation of the K-ras oncogene causes early onset lung cancer in mice. Nature. 2001; 410: 1111-1116.

[78] Kim M, Mun H, Sung CO, et al. Patient-derived lung cancer organoids as in vitro cancer models for therapeutic screening. Nat Commun. 2019; 10: 3991.

[79] Li J, Chen F, Peng Y, et al. N6-methyladenosine regulates the expression and secretion of TGFβ1 to affect the epithelial-mesenchymal transition of cancer cells. Cells. 2020; 9(2): 296.

[80] Chen Z, Zhou J, Wu Y, et al. METTL3 promotes cellular senescence of colorectal cancer via modulation of CDKN2B transcription and mRNA stability. Oncogene. 2024; 43: 976-991.

[81] Guo W, Zhou B, Bie F, et al. Single-cell RNA sequencing analysis reveals transcriptional heterogeneity of multiple primary lung cancer. Clin Transl Med. 2023; 13: e1453.

[82] Zeng Q, Saghafinia S, Chryplewicz A, et al. Aberrant hyperexpression of the RNA binding protein FMRP in tumors mediates immune evasion. Science. 2022; 378: eabl7207.

[83] Barbie DA, Tamayo P, Boehm JS, et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009; 462: 108-112.

[84] He H, Li Z, Lu J, et al. Single-cell RNA-seq reveals clonal diversity and prognostic genes of relapsed multiple myeloma. Clin Transl Med. 2022; 12: e757.

RIGHTS & PERMISSIONS

2025 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.