METTL3 enhances the stability of MALAT1 with the assistance of HuR via m6A modification and activates NF-κB to promote the malignant progression of IDH-wildtype glioma

Highlights

• METTL3 plays an oncogenic role in IDH-wildtype gliomas.

• METTL3 enhances MALAT1 RNA stabilization via m⁶A.

• HuR is essential for METTL3-mediated MALAT1 RNA stabilization.

• MALAT1 activates NF-κB.

Abstract

Understanding the role of N6-methyladenosine (m⁶A) in tumorigenesis and stem cell maintenance is an emerging field in glioma research. However, it is necessary to study the function of m⁶A in IDH-mutation and IDH-wildtype gliomas separately. Here, we aimed to elucidate the role and mechanism of the m⁶A writer METTL3 in regulating the malignant progression of IDH-wildtype gliomas. We demonstrated that METTL3 expression is positively associated with a higher malignant grade and poorer prognosis of IDH-wildtype gliomas but not IDH-mutant gliomas. METTL3 could also promote the malignant progression of gliomas in both in vitro and in vivo models. Mechanistically, METTL3 upregulated MALAT1 expression by enhancing its stability via m⁶A modification. We further revealed that HuR was essential for METTL3-mediated MALAT1 stabilization, and upregulated MALAT1 subsequently activated NF-κB. Taken together, our findings confirmed that METTL3 promoted the malignant progression of IDH-wildtype gliomas and revealed important insight into the upstream regulatory mechanism of MALAT1 and NF-κB with a primary focus on m6A modification.

Introduction

Glioma is the most common primary fatal tumor in the central nervous system (CNS) [[1], [2], [3]]. Based on the latest World Health Organization classification of CNS tumors, gliomas can be classified as IDH-wildtype and IDH-mutant [4]. Compared with IDH-mutant gliomas, IDH-wildtype gliomas have poorer clinical outcomes, and the median overall survival (OS) for patients with IDH-wildtype glioblastoma (GBM) is only approximately 14–16 months [1]. Extensive studies have demonstrated that molecular features, epigenetic characteristics, and RNA profiles are also different between IDH-mutant and IDH-wildtype gliomas [[5], [6], [7], [8]]. Thus, it is necessary to study the mechanism underlying the malignant progression of IDH mutation and wildtype glioma separately.

It has been revealed that aberrant RNA expression is involved in the malignant progression of gliomas [2,9,10]. RNA expression levels are largely determined by epigenetic regulatory mechanisms. In addition to protein modification and DNA methylation, RNA methylation is an emerging field of epigenetic research [[11], [12], [13], [14]]. N6-methyladenosine (m⁶A) is the most abundant form of mRNA and long noncoding RNA (lncRNA) methylation in eukaryotic cells [[14], [15], [16]]. Studies have revealed that the m⁶A level could impact the entire RNA life cycle, including alternative polyadenylation, pre-RNA processing, RNA export from the nucleus to the cytoplasm, RNA stability, and mRNA translation [6,[17], [18], [19], [20], [21], [22]]. The m⁶A level is dynamically regulated by its regulators, including methyltransferases (writers), binding proteins (readers), and demethylases (erasers) [21]. Currently, the widely recognized m⁶A writers include METTL3, METTL14, WTAP, KIAA1429, RBM15, and ZC3H13; the erasers include FTO and ALKBH5; and the readers mainly include YTHDC1, YTHDC2, YTHDF1, YTHDF2, YTHDF3, and HNRNPC [2,21]. In addition, Hu Antigen R/ELAV Like RNA Binding Protein 1 (HuR/ELAVL1) and EIF3 proteins can recognize and bind m6A-modified transcripts [23,24].

Studies on m⁶A regulators have greatly enhanced our understanding of the physiological and pathological functions of m⁶A modification [14,20]. Several studies have shown that m⁶A modification plays important roles in the maintenance of stem cell properties and therapeutic resistance of gliomas [23,25,26]. Some of these studies demonstrated that METTL3 knockdown could suppress glioblastoma stem cells (GSCs) by regulating mRNA m⁶A enrichment and the expression levels of targets, such as ADAM19, SOX2, and SRSF [23,25]. However, another group reported that METTL3 knockdown dramatically promoted GSC self-renewal and tumorigenesis [26]. Whether METTL3 is an oncogene or anti-oncogene in gliomas remains to be clarified. Our recent study showed that METTL3 expression is highly associated with the IDH status of glioma [2]. Another study also revealed that FTO is upregulated in IDH-mutant leukemia and plays an anti-tumor role through the FTO/m⁶A/MYC/CEBPA signaling pathway [27]. Together, these data suggested that the role of METTL3 should be studied separately in gliomas with different IDH statuses.

Here, to further clarify the role of METTL3 in IDH-wildtype gliomas, we systemically analyzed the expression of METTL3 and its prognosis value in glioma patients in both the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets. We observed that METTL3 expression was positively correlated with increasing malignant degrees of IDH-wildtype gliomas but not IDH-mutant gliomas. Then, we demonstrated that METTL3 could promote cell proliferation and migration in several IDH-wildtype glioma cell models. Furthermore, we revealed that elevated METTL3 expression could enhance the stability of MALAT1 with the assistance of HuR through m6A modification and then activate the NF-κB signaling pathway. Finally, we also validated the role of METTL3 in promoting tumor progression and activating NF-κB signaling in orthotopic xenograft models.