Genome-wide profiling of N6-methyladenosine-modified pseudogene-derived long noncoding RNAs reveals the tumour-promoting and innate immune-restraining function of RPS15AP12 in ovarian cancer

Jie Xu , Yifei Ren , Jiayi Lu , Fengjiang Qin , Dan Yang , Chunyan Tang , Yu Yang , Jing Xu , Tao Liu , Ping Yi

Clinical and Translational Medicine ›› 2025, Vol. 15 ›› Issue (3) : e70249

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Clinical and Translational Medicine ›› 2025, Vol. 15 ›› Issue (3) : e70249 DOI: 10.1002/ctm2.70249
RESEARCH ARTICLE

Genome-wide profiling of N6-methyladenosine-modified pseudogene-derived long noncoding RNAs reveals the tumour-promoting and innate immune-restraining function of RPS15AP12 in ovarian cancer

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Abstract

•Genome-wide profiling reveals the redistribution of m6A modification on pseudogene-derived lncRNAs and m6A redistribution-relevant dysregulation of pseudogenes in HGSOC.

•RPS15AP12, as a representative processed pseudogene, is up-regulated by FTO-mediated demethylation and acts as a miRNA sponge to promote RPS15A expression via competitively binding to miR-96-3p.

•RPS15AP12/RPS15A axis inhibits MAVS sensors (RIG-I and MDA5) and downstream IFN-β levels in ovarian cancer.

Keywords

innate immune response / m 6A / miRNA sponge / ovarian cancer / pseudogene

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Jie Xu, Yifei Ren, Jiayi Lu, Fengjiang Qin, Dan Yang, Chunyan Tang, Yu Yang, Jing Xu, Tao Liu, Ping Yi. Genome-wide profiling of N6-methyladenosine-modified pseudogene-derived long noncoding RNAs reveals the tumour-promoting and innate immune-restraining function of RPS15AP12 in ovarian cancer. Clinical and Translational Medicine, 2025, 15(3): e70249 DOI:10.1002/ctm2.70249

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References

[1]

Karreth FA, Reschke M, Ruocco A, et al. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell. 2015;161(2):319-332.

[2]

Cheetham SW, Faulkner GJ, Dinger ME. Overcoming challenges and dogmas to understand the functions of pseudogenes. Nat Rev Genet. 2020;21(3):191-201.

[3]

Ma Y, Liu S, Gao J, et al. Genome-wide analysis of pseudogenes reveals HBBP1’s human-specific essentiality in erythropoiesis and implication in β-thalassemia. Dev Cell. 2021;56(4):478-493.e11.

[4]

Han L, Yuan Y, Zheng S, et al. The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes. Nat Commun. 2014;5:3963.

[5]

Chiang JJ, Sparrer KMJ, van Gent M, et al. Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I-mediated immunity. Nat Immunol. 2018;19(1):53-62.

[6]

Rapicavoli NA, Qu K, Zhang J, Mikhail M, Laberge RM, Chang HY. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. Elife 2013;2;e00762.

[7]

Zhang F, Liu S, Qiao Z, et al. Housekeeping U1 snRNA facilitates antiviral innate immunity by promoting TRIM25-mediated RIG-I activation. Cell Rep. 2024;43(3):113945.

[8]

Zhou Z, Chen MM, Luo Y, et al. Tumor-intrinsic SIRPA promotes sensitivity to checkpoint inhibition immunotherapy in melanoma. Cancer Cell. 2022;40(11):1324-1340.e8.

[9]

Han YJ, Zhang J, Lee JH, et al. The BRCA1 pseudogene negatively regulates antitumor responses through inhibition of innate immune defense mechanisms. Cancer Res. 2021;81(6):1540-1551.

[10]

Amaral P, Carbonell-Sala S, De La, et al. The status of the human gene catalogue. Nature. 2023;622(7981):41-47.

[11]

Tan L, Cheng W, Liu F, et al. Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes. Genome Biol. 2021;22(1):180.

[12]

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(7540):560-564.

[13]

Ping XL, Sun BF, Wang L, et al. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 2014;24(2):177-189.

[14]

Kasowitz SD, Ma J, Anderson SJ, et al. Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development. PLoS Genet. 2018;14(5):e1007412.

[15]

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(12):1403-1419.

[16]

Haussmann IU, Bodi Z, Sanchez-Moran E, et al. m(6)A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination. Nature. 2016;540(7632):301-304.

[17]

Kuroki L, Guntupalli SR. Treatment of epithelial ovarian cancer. BMJ 2020;371;m3773.

[18]

Cress RD, Chen YS, Morris CR, Petersen M, Leiserowitz GS. Characteristics of long-term survivors of epithelial ovarian cancer. Obstet Gynecol. 2015;126(3):491-497.

[19]

Wang Y, Duval AJ, Adli M, Matei D. Biology-driven therapy advances in high-grade serous ovarian cancer. J Clin Invest. 2024;134(1):e174013.

[20]

Tian X, Song J, Zhang X, et al. MYC-regulated pseudogene HMGA1P6 promotes ovarian cancer malignancy via augmenting the oncogenic HMGA1/2. Cell Death Dis. 2020;11(3):167.

[21]

Wang X, Li X, Lin F, et al. The lnc-CTSLP8 upregulates CTSL1 as a competitive endogenous RNA and promotes ovarian cancer metastasis. J Exp Clin Cancer Res. 2021;40(1):151.

[22]

Zhao H, Wang A, Zhang Z. LncRNA SDHAP1 confers paclitaxel resistance of ovarian cancer by regulating EIF4G2 expression via miR-4465. J Biochem. 2020;168(2):171-181.

[23]

Guo P, Wang Y, Dai C, et al. Ribosomal protein S15a promotes tumor angiogenesis via enhancing Wnt/β-catenin-induced FGF18 expression in hepatocellular carcinoma. Oncogene. 2018;37(9):1220-1236.

[24]

Liu C, He X, Liu X, et al. RPS15A promotes gastric cancer progression via activation of the Akt/IKK-beta/NF-kappaB signalling pathway. J Cell Mol Med. 2019;23(3):2207-2218.

[25]

Chen J, Wei Y, Feng Q, et al. Ribosomal protein S15A promotes malignant transformation and predicts poor outcome in colorectal cancer through misregulation of p53 signaling pathway. Int J Oncol. 2016;48(4):1628-1638.

[26]

Zhang Z, Zhan Q, Eckert M, et al. RADAR: differential analysis of MeRIP-seq data with a random effect model. Genome Biol. 2019;20(1):294.

[27]

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37(8):907-915.

[28]

Meng J, Lu Z, Liu H, et al. A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. Methods. 2014;69(3):274-281.

[29]

Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576-589.

[30]

Ramírez F, Ryan DP, Grüning B, et al. deepTools2:a next generation web server for deep-sequencing data analysis. Nucleic Acids Res 2016;44(W1):W160-W165.

[31]

Bailey TL. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics. 2011;27(12):1653-1659.

[32]

Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841-842.

[33]

Liu Z, Gao L, Cheng L, et al. The roles of N6-methyladenosine and its target regulatory noncoding RNAs in tumors: classification, mechanisms, and potential therapeutic implications. Exp Mol Med. 2023;55(3):487-501.

[34]

Duan JL, Chen W, Xie JJ, et al. A novel peptide encoded by N6-methyladenosine modified circMAP3K4 prevents apoptosis in hepatocellular carcinoma. Mol Cancer. 2022;21(1):93.

[35]

Xu J, Wan Z, Tang M, et al. N(6)-methyladenosine-modified CircRNA-SORE sustains sorafenib resistance in hepatocellular carcinoma by regulating β-catenin signaling. Mol Cancer. 2020;19(1):163.

[36]

Wu P, Fang X, Liu Y, et al. N6-methyladenosine modification of circCUX1 confers radioresistance of hypopharyngeal squamous cell carcinoma through caspase1 pathway. Cell Death Dis. 2021;12(4):298.

[37]

Chen Z, Ling K, Zhu Y, Deng L, Li Y, Liang Z. circ0000069 promotes cervical cancer cell proliferation and migration by inhibiting miR-4426. Biochem Biophys Res Commun. 2021;551:114-120.

[38]

Lin C, Ma M, Zhang Y, et al. The N(6)-methyladenosine modification of circALG1 promotes the metastasis of colorectal cancer mediated by the miR-342-5p/PGF signalling pathway. Mol Cancer. 2022;21(1):80.

[39]

Wang T, Liu Z, She Y, et al. A novel protein encoded by circASK1 ameliorates gefitinib resistance in lung adenocarcinoma by competitively activating ASK1-dependent apoptosis. Cancer Lett. 2021;520:321-331.

[40]

Rao X, Lai L, Li X, Wang L, Li A, Yang Q. N(6) -methyladenosine modification of circular RNA circ-ARL3 facilitates Hepatitis B virus-associated hepatocellular carcinoma via sponging miR-1305. IUBMB Life. 2021;73(2):408-417.

[41]

Chen C, Yuan W, Zhou Q, et al. N6-methyladenosine-induced circ1662 promotes metastasis of colorectal cancer by accelerating YAP1 nuclear localization. Theranostics. 2021;11(9):4298-4315.

[42]

Liu Z, Wang T, She Y, et al. N(6)-methyladenosine-modified circIGF2BP3 inhibits CD8(+) T-cell responses to facilitate tumor immune evasion by promoting the deubiquitination of PD-L1 in non-small cell lung cancer. Mol Cancer. 2021;20(1):105.

[43]

Zhang J, Bai R, Li M, et al. Excessive miR-25-3p maturation via N(6)-methyladenosine stimulated by cigarette smoke promotes pancreatic cancer progression. Nat Commun. 2019;10(1):1858.

[44]

Liu T, Li P, Li J, et al. Exosomal and intracellular miR-320b promotes lymphatic metastasis in esophageal squamous cell carcinoma. Mol Ther Oncolytics. 2021;23:163-180.

[45]

Alarcón CR, Goodarzi H, Lee H, Liu X, Tavazoie S, Tavazoie SF. HNRNPA2B1 is a mediator of m(6)A-dependent nuclear RNA processing events. Cell. 2015;162(6):1299-1308.

[46]

Yin H, Chen L, Piao S, et al. M6A RNA methylation-mediated RMRP stability renders proliferation and progression of non-small cell lung cancer through regulating TGFBR1/SMAD2/SMAD3 pathway. Cell Death Differ. 2023;30(3):605-617.

[47]

Wu J, Pang R, Li M, Chen B, Huang J, Zhu Y. m6A-Induced LncRNA MEG3 suppresses the proliferation, migration and invasion of hepatocellular carcinoma cell through miR-544b/BTG2 signaling. Onco Targets Ther. 2021;14:3745-3755.

[48]

Wu Y, Yang X, Chen Z, et al. A-induced lncRNA RP11 triggers the dissemination of colorectal cancer cells via upregulation of Zeb1. Mol Cancer. 2019;18(1):87.

[49]

Zhao R, Li B, Zhang S, et al. The N(6)-Methyladenosine-Modified pseudogene HSPA7 correlates with the tumor microenvironment and predicts the response to immune checkpoint therapy in glioblastoma. Front Immunol. 2021;12:653711.

[50]

Tan L, Qin Y, Xie R, et al. N6-methyladenosine-associated prognostic pseudogenes contribute to predicting immunotherapy benefits and therapeutic agents in head and neck squamous cell carcinoma. Theranostics. 2022;12(17):7267-7288.

[51]

Deng J, Zhang J, Ye Y, et al. N(6)-methyladenosine-mediated upregulation of WTAPP1 promotes WTAP translation and Wnt signaling to facilitate pancreatic cancer progression. Cancer Res. 2021;81(20):5268-5283.

[52]

Liu S, Chen X, Huang K, et al. Long noncoding RNA RFPL1S-202 inhibits ovarian cancer progression by downregulating the IFN-β/STAT1 signaling. Exp Cell Res. 2023;422(2):113438.

[53]

Wang H, Liu J, Zhu X, Yang B, He Z, Yao X. AZGP1P2/UBA1/RBM15 cascade mediates the fate determinations of prostate cancer stem cells and promotes therapeutic effect of docetaxel in castration-resistant prostate cancer via TPM1 m6A modification. Research (Wash D C). 2023;6:0252.

[54]

Karreth FA, Pandolfi PP. ceRNA cross-talk in cancer: when ce-bling rivalries go awry. Cancer Discov. 2013;3(10):1113-1121.

[55]

Qi P, Zhou XY, Du X. Circulating long non-coding RNAs in cancer: current status and future perspectives. Mol Cancer. 2016;15(1):39.

[56]

Kwon J, Liu YV, Gao C, et al. Pseudogene-mediated DNA demethylation leads to oncogene activation. Sci Adv. 2021;7(40):eabg1695.

[57]

Vaid R, Thombare K, Mendez A, et al. METTL3 drives telomere targeting of TERRA lncRNA through m6A-dependent R-loop formation: a therapeutic target for ALT-positive neuroblastoma. Nucleic Acids Res. 2024;52(5):2648-2671.

[58]

Arab K, Park YJ, Lindroth AM, et al. Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A. Mol Cell. 2014;55(4):604-614.

[59]

Tenorio M, Cruz-Ruiz S, Encarnación-Guevara S, et al. MAYEX is an old long noncoding RNA recruited for X chromosome dosage compensation in a reptile. Science. 2024;385(6715):1347-1354.

[60]

Arab K, Karaulanov E, Musheev M, et al. GADD45A binds R-loops and recruits TET1 to CpG island promoters. Nat Genet. 2019;51(2):217-223.

[61]

Lan Y, Xiao X, He Z, et al. Long noncoding RNA OCC-1 suppresses cell growth through destabilizing HuR protein in colorectal cancer. Nucleic Acids Res. 2018;46(11):5809-5821.

[62]

Liao M, Liao W, Xu N, et al. LncRNA EPB41L4A-AS1 regulates glycolysis and glutaminolysis by mediating nucleolar translocation of HDAC2. EBioMedicine. 2019;41:200-213.

[63]

Yang H, Li M, Qi Y. FOXN3 inhibits the progression of ovarian cancer through negatively regulating the expression of RPS15A. Hum Cell. 2023;36(3):1120-1134.

[64]

Ran XB, Ding LW, Sun QY, et al. Targeting RNA exonuclease XRN1 potentiates efficacy of cancer immunotherapy. Cancer Res. 2023;83(6):922-938.

[65]

Hu A, Sun L, Lin H, Liao Y, Yang H, Mao Y. Harnessing innate immune pathways for therapeutic advancement in cancer. Signal Transduct Target Ther. 2024;9(1):68.

[66]

Chiappinelli KB, Strissel PL, Desrichard A, et al. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. Cell. 2015;162(5):974-986.

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

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