N-acetyltransferase 10 facilitates tumorigenesis of diffuse large B-cell lymphoma by regulating AMPK/mTOR signalling through N4-acetylcytidine modification of SLC30A9

Abstract

Background: Accumulating studies suggested that posttranscriptional modifications exert a vital role in the tumorigenesis of diffuse large B-cell lymphoma (DLBCL). N4-acetylcytidine (ac4C) modification, catalyzed by the N-acetyltransferase 10 (NAT10), was a novel type of chemical modification that improves translation efficiency and mRNA stability.

Methods: GEO databases and clinical samples were used to explore the expression and clinical value of NAT10 in DLBCL. CRISPER/Cas9-mediated knockout of NAT10 was performed to determine the biological functions of NAT10 in DLBCL. RNA sequencing, acetylated RNA immunoprecipitation sequencing (acRIP-seq), LC-MS/MS, RNA immunoprecipitation (RIP)-qPCR and RNA stability assays were performed to explore the mechanism by which NAT10 contributed to DLBCL progression.

Results: Here, we demonstrated that NAT10-mediated ac4C modification regulated the occurrence and progression of DLBCL. Dysregulated N-acetyltransferases expression was found in DLBCL samples. High expression of NAT10 was associated with poor prognosis of DLBCL patients. Deletion of NAT10 expression inhibited cell proliferation and induced G0/G1 phase arrest. Furthermore, knockout of NAT10 increased the sensitivity of DLBCL cells to ibrutinib. AcRIP-seq identified solute carrier family 30 member 9 (SLC30A9) as a downstream target of NAT10 in DLBCL. NAT10 regulated the mRNA stability of SLC30A9 in an ac4C-dependent manner. Genetic silencing of SLC30A9 suppressed DLBCL cell growth via regulating the activation of AMP-activated protein kinase (AMPK) pathway.

Conclusion: Collectively, these findings highlighted the essential role of ac4C RNA modification mediated by NAT10 in DLBCL, and provided insights into novel epigenetic-based therapeutic strategies.

Keywords

Diffuse large B-cell lymphoma / N4-acetyclytidine / N-acetyltransferase 10 / Solute carrier family 30 member 9

References

[1] Schmitz R, Wright GW, Huang DW, et al. Genetics and pathogenesis of diffuse large B-cell lymphoma. N Engl J Med. 2018;378:1396-1407.

[2] Liu Y, Barta SK. Diffuse large B-cell lymphoma: 2019 update on diagnosis, risk stratification, and treatment. Am J Hematol. 2019;94:604-616.

[3] Cai Y, Chen X, Lu T, et al. Activation of STING by SAMHD1 deficiency promotes PANoptosis and enhances efficacy of PD-L1 blockade in diffuse large B-cell lymphoma. Int J Biol Sci. 2023;19:4627-4643.

[4] Carpio C, Bouabdallah R, Ysebaert L, et al. Avadomide monotherapy in relapsed/refractory DLBCL: safety, efficacy, and a predictive gene classifier. Blood. 2020;135:996-1007.

[5] Hu S, Ren S, Cai Y, et al. Glycoprotein PTGDS promotes tumorigenesis of diffuse large B-cell lymphoma by MYH9-mediated regulation of Wnt-β-catenin-STAT3 signaling. Cell Death Differ. 2022;29:642-656.

[6] Chen X, Lu T, Ding M, et al. Targeting YTHDF2 inhibits tumorigenesis of diffuse large B-cell lymphoma through ACER2-mediated ceramide catabolism. J Adv Res. 2023:S2090-1232(23)00314-4.

[7] Bakhshi TJ, Georgel PT. Genetic and epigenetic determinants of diffuse large B-cell lymphoma. Blood Cancer J. 2020;10:123.

[8] Oricchio E. Epigenetic balance in DLBCL. Blood. 2021;138:355-356.

[9] Barbieri I, Kouzarides T. Role of RNA modifications in cancer. Nat Rev Cancer. 2020;20:303-322.

[10] Yang W, Li HY, Wu YF, et al. ac4C acetylation of RUNX2 catalyzed by NAT10 spurs osteogenesis of BMSCs and prevents ovariectomy-induced bone loss. Mol Ther Nucleic Acids. 2021;26:135-147.

[11] Jin G, Xu M, Zou M, Duan S. The processing, gene regulation, biological functions, and clinical relevance of N4-acetylcytidine on RNA: a systematic review. Mol Ther Nucleic Acids. 2020;20:13-24.

[12] Stern L, Schulman LH. The role of the minor base N4-acetylcytidine in the function of the Escherichia coli noninitiator methionine transfer RNA. J Biol Chem. 1978;253:6132-6139.

[13] Bortolin-Cavaillé M-L, Quillien A, Thalalla Gamage S, et al. Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution. Nucleic Acids Res. 2022;50:6284-6299.

[14] Broly M, Polevoda BV, Awayda KM, et al. THUMPD1 bi-allelic variants cause loss of tRNA acetylation and a syndromic neurodevelopmental disorder. Am J Hum Genet. 2022;109:587-600.

[15] Arango D, Sturgill D, Alhusaini N, et al. Acetylation of cytidine in mRNA promotes translation efficiency. Cell. 2018;175:1872-1886 e1824.

[16] Zhang Y, Jing Y, Wang Y, et al. NAT10 promotes gastric cancer metastasis via N4-acetylated COL5A1. Signal Transduct Target Ther. 2021;6(1):173.

[17] Jin C, Wang T, Zhang D, et al. Acetyltransferase NAT10 regulates the Wnt/β-catenin signaling pathway to promote colorectal cancer progression via ac(4)C acetylation of KIF23 mRNA. J Exp Clin Cancer Res. 2022;41:345.

[18] Wei R, Cui X, Min J, et al. NAT10 promotes cell proliferation by acetylating CEP170 mRNA to enhance translation efficiency in multiple myeloma. Acta Pharm Sin B. 2022;12:3313-3325.

[19] Deng M, Zhang L, Zheng W, et al. Helicobacter pylori-induced NAT10 stabilizes MDM2 mRNA via RNA acetylation to facilitate gastric cancer progression. J Exp Clin Cancer Res. 2023;42:9.

[20] Xie R, Cheng L, Huang M, et al. NAT10 drives cisplatin chemoresistance by enhancing ac4C-associated DNA repair in bladder cancer. Cancer Res. 2023;83(10):1666-1683.

[21] Chen L, Wang W-J, Liu Q, et al. NAT10-mediated N4-acetylcytidine modification is required for meiosis entry and progression in male germ cells. Nucleic Acids Res. 2022;50:10896-10913.

[22] Liu H-Y, Liu Y-Y, Yang F, et al. Acetylation of MORC2 by NAT10 regulates cell-cycle checkpoint control and resistance to DNA-damaging chemotherapy and radiotherapy in breast cancer. Nucleic Acids Res. 2020;48(7):3638-3656.

[23] Cao Y, Yao M, Wu Y, Ma N, Liu H, Zhang B. N-acetyltransferase 10 promotes micronuclei formation to activate the senescence-associated secretory phenotype machinery in colorectal cancer cells. Transl Oncol. 2020;13:100783.

[24] Zhang X, Chen J, Jiang S, et al. N-acetyltransferase 10 enhances doxorubicin resistance in human hepatocellular carcinoma cell lines by promoting the epithelial-to-mesenchymal transition. Oxid Med Cell Longev. 2019;2019:7561879.

[25] Pan Z, Bao Y, Hu M, et al. Role of NAT10-mediated ac4C-modified HSP90AA1 RNA acetylation in ER stress-mediated metastasis and lenvatinib resistance in hepatocellular carcinoma. Cell Death Discovery. 2023;9:56.

[26] Jiang X, Cheng Yu, Zhu Y, et al. Maternal NAT10 orchestrates oocyte meiotic cell-cycle progression and maturation in mice. Nat Commun. 2023;14:3729.

[27] Chen Y-H, Yang CK, Xia M, Ou C-Y, Stallcup MR. Role of GAC63 in transcriptional activation mediated by beta-catenin. Nucleic Acids Res. 2007;35:2084-2092.

[28] Xie S, Wei F, Sun Y-M, et al. EZH2 inhibitors abrogate upregulation of trimethylation of H3K27 by CDK9 inhibitors and potentiate its activity against diffuse large B-cell lymphoma. Haematologica. 2020;105:1021-1031.

[29] Zheng X, Wang Q, Zhou Y, et al. N-acetyltransferase 10 promotes colon cancer progression by inhibiting ferroptosis through N4-acetylation and stabilization of ferroptosis suppressor protein 1 (FSP1) mRNA. Cancer Commun. 2022;42:1347-1366.

[30] Wang G, Zhang M, Zhang Y, et al. NAT10-mediated mRNA N4-acetylcytidine modification promotes bladder cancer progression. Clin Transl Med. 2022;12:e738.

[31] Larrieu D, Britton S, Demir M, Rodriguez R, Jackson SP. Chemical inhibition of NAT10 corrects defects of laminopathic cells. Science. 2014;344:527-532.

[32] Tsai K, Jaguva Vasudevan AA, Martinez Campos C, Emery A, Swanstrom R, Cullen BR. Acetylation of cytidine residues boosts HIV-1 gene expression by increasing viral RNA stability. Cell Host Microbe. 2020;28:306-312.

[33] Sharma S, Langhendries J-L, Watzinger P, Kötter P, Entian K-D, Lafontaine DLJ. Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. Nucleic Acids Res. 2015;43:2242-2258.

[34] Deng H, Qiao X, Xie T, et al. SLC-30A9 is required for Zn²⁺ homeostasis, Zn²⁺ mobilization, and mitochondrial health. Proc Natl Acad Sci U S A. 2021;118(35):e2023909118.

[35] Mihaylova MM, Shaw RJ. The AMPK signalling pathway coordinates cell growth, autophagy and metabolism. Nat Cell Biol. 2011;13:1016-1023.

[36] Zi J, Han Qi, Gu S, et al. Targeting NAT10 induces apoptosis associated with enhancing endoplasmic reticulum stress in acute myeloid leukemia cells. Front Oncol. 2020;10:598107.

[37] Wang E, Mi X, Thompson MC, et al. Mechanisms of resistance to noncovalent Bruton's tyrosine kinase inhibitors. N Engl J Med. 2022;386:735-743.

[38] Pan Z, Scheerens H, Li S-J, et al. Discovery of selective irreversible inhibitors for Bruton's tyrosine kinase. ChemMedChem. 2007;2:58-61.

[39] Noy A, De Vos S, Coleman M, et al. Durable ibrutinib responses in relapsed/refractory marginal zone lymphoma: long-term follow-up and biomarker analysis. Blood Adv. 2020;4:5773-5784.

[40] Wilson WH, Young RM, Schmitz R, et al. Targeting B cell receptor signaling with ibrutinib in diffuse large B cell lymphoma. Nat Med. 2015;21:922-926.

[41] Witzens-Harig M, Viardot A, Keller U, et al. The mTOR inhibitor temsirolimus added to rituximab combined with dexamethasone, cytarabine, and cisplatinum (R-DHAP) for the treatment of patients with relapsed or refractory DLBCL—results from the phase-II STORM trial. Hemasphere. 2021;5:e636.

[42] Neganova ME, Klochkov SG, Aleksandrova YR, Aliev G. Histone modifications in epigenetic regulation of cancer: perspectives and achieved progress. Semin Cancer Biol. 2022;83:452-471.

[43] Cai Y, Feng R, Lu T, Chen X, Zhou X, Wang X. Novel insights into the m(6)A-RNA methyltransferase METTL3 in cancer. Biomark Res. 2021;9:27.

[44] Nombela P, Miguel-López B, Blanco S. The role of m⁶A, m⁵C and Ψ RNA modifications in cancer: novel therapeutic opportunities. Mol Cancer. 2021;20:18.

[45] Arango D, Sturgill D, Yang R, et al. Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine. Mol Cell. 2022;82:2797-2814.

[46] Yang Q, Lei X, He J, et al. N4-acetylcytidine drives glycolysis addiction in gastric cancer via NAT10/SEPT9/HIF-1α positive feedback loop. Adv Sci (Weinh). 2023;10(23):e2300898.

[47] Johansson MJO, Byström AS. The Saccharomyces cerevisiae TAN1 gene is required for N4-acetylcytidine formation in tRNA. RNA. 2004;10:712-719.

[48] Thomas G, Gordon J, Rogg H. N4-acetylcytidine. A previously unidentified labile component of the small subunit of eukaryotic ribosomes. J Biol Chem. 1978;253:1101-1105.

[49] Xie R, Cheng L, Huang M, et al. NAT10 drives cisplatin chemoresistance by enhancing ac4C-associated DNA repair in bladder cancer. Cancer Res. 2023;83:1666-1683.

[50] Csikós A, Kozma B, Pór Á, et al. Zinc transporter 9 (SLC30A9) expression is decreased in the vaginal tissues of menopausal women. Biol Trace Elem Res. 2021;199:4011-4019.

[51] Burger JA, Barr PM, Robak T, et al. Long-term efficacy and safety of first-line ibrutinib treatment for patients with CLL/SLL: 5 years of follow-up from the phase 3 RESONATE-2 study. Leukemia. 2020;34:787-798.

[52] Le Gouill S, Morschhauser F, Chiron D, et al. Ibrutinib, obinutuzumab, and venetoclax in relapsed and untreated patients with mantle cell lymphoma: a phase 1/2 trial. Blood. 2021;137:877-887.

[53] Stewart CM, Michaud L, Whiting K, et al. Phase I/Ib study of the efficacy and safety of buparlisib and ibrutinib therapy in MCL, FL, and DLBCL with serial cell-free DNA monitoring. Clin Cancer Res. 2022;28:45-56.

[54] Chen X, Hao Y, Liu Y, et al. NAT10/ac4C/FOXP1 promotes malignant progression and facilitates immunosuppression by reprogramming glycolytic metabolism in cervical cancer. Adv Sci (Weinh). 2023;10:e2302705.

[55] Liu Y, Wang X, Liu Y, et al. N4-acetylcytidine-dependent GLMP mRNA stabilization by NAT10 promotes head and neck squamous cell carcinoma metastasis and remodels tumor microenvironment through MAPK/ERK signaling pathway. Cell Death Dis. 2023;14:712.

[56] Chen X, Lu T, Cai Y, et al. KIAA1429-mediated m6A modification of CHST11 promotes progression of diffuse large B-cell lymphoma by regulating Hippo-YAP pathway. Cell Mol Biol Lett. 2023;28:32.

RIGHTS & PERMISSIONS

2024 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.