The roles and implications of RNA m6A modification in cancer

Abstract

N⁶-Methyladenosine (m⁶A), the most prevalent internal modification in eukaryotic mRNA, has been extensively and increasingly studied over the past decade. Dysregulation of RNA m⁶A modification and its associated machinery, including writers, erasers and readers, is frequently observed in various cancer types, and the dysregulation profiles might serve as diagnostic, prognostic and/or predictive biomarkers. Dysregulated m⁶A modifiers have been shown to function as oncoproteins or tumour suppressors with essential roles in cancer initiation, progression, metastasis, metabolism, therapy resistance and immune evasion as well as in cancer stem cell self-renewal and the tumour microenvironment, highlighting the therapeutic potential of targeting the dysregulated m⁶A machinery for cancer treatment. In this Review, we discuss the mechanisms by which m⁶A modifiers determine the fate of target RNAs and thereby influence protein expression, molecular pathways and cell phenotypes. We also describe the state-of-the-art methodologies for mapping global m⁶A epitranscriptomes in cancer. We further summarize discoveries regarding the dysregulation of m⁶A modifiers and modifications in cancer, their pathological roles, and the underlying molecular mechanisms. Finally, we discuss m⁶A-related prognostic and predictive molecular biomarkers in cancer as well as the development of small-molecule inhibitors targeting oncogenic m⁶A modifiers and their activity in preclinical models.

Figure 1.. RNA m⁶A machinery and various aspects of RNA fates regulated by m⁶A methylation.

The installation of m⁶A methylation for most mRNA transcripts is fulfilled by the methyltransferase complex (MTC) comprising a core complex and other accessory subunits. Methyltransferase (METTL) 3, METTL14, and WT1 associated protein (WTAP) constitute the core complex. Other “writers” apart from the MTC, such as METTL16, phosphorylated CTD interacting factor 1 (PCIF1), and METTL5, govern m⁶A deposition for their own specific targets. Two “eraser” proteins, FTO alpha-ketoglutarate dependent dioxygenase (FTO) and alkB homolog 5, RNA demethylase (ALKBH5), are responsible for demethylation of m⁶A-modified RNAs. The chemical structure of m⁶A is shown (bottom left), with its methyl group highlighted. A variety of m⁶A reader proteins, represented by the YT521-B homology (YTH) family, the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family, and the heterogeneous nuclear ribonucleoprotein (HNRNP) family, specifically recognize m⁶A marks and mediate the regulation of various aspects of target RNA fates, including RNA stability, translation, splicing, and nuclear export. Respective reader proteins involved in these aspects are listed and indicated for their roles when applicable (upward arrow indicates a promoting role and downward arrow indicates an inhibitory role).

Figure 2a.. Oncogenic functions of m⁶A modifiers in cancer.

Tumour-promoting m⁶A modifiers (including writers, erasers and readers) and their representative downstream targets, including coding and non-coding RNAs, are illustrated. Positive targets of m⁶A modifiers are in red, while negative targets of m⁶A modifiers are in blue. METTL3, methyltransferase 3; METTL14, methyltransferase14; WTAP, WT1 associated protein; METTL16, methyltransferase16; FTO, FTO alpha-ketoglutarate dependent dioxygenase; ALKBH5, alkB homolog 5; YTHDF1, YTH N6-Methyladenosine RNA Binding Protein 1; YTHDF2, YTH N6-Methyladenosine RNA Binding Protein 2; YTHDF3, YTH N6-Methyladenosine RNA Binding Protein 3;YTHDC1, YTH domain-containing protein 1; YTHDC2, YTH domain-containing protein 2; IGF2BP1, Insulin-like growth factor 2 mRNA-binding protein 1; IGF2BP2, Insulin-like growth factor 2 mRNA-binding protein 2; IGF2BP3, Insulin-like growth factor 2 mRNA-binding protein 3.

Figure 2b.. Tumour suppressive functions of m⁶A modifiers in cancer.

Tumour-suppressing m⁶A modifiers and their representative downstream targets, including coding and non-coding RNAs, are illustrated. Positive targets of m⁶A modifiers are in red, while negative targets of m⁶A modifiers are in blue. METTL3, methyltransferase 3; METTL14, methyltransferase14; WTAP, WT1 associated protein; METTL16, methyltransferase16; FTO, FTO alpha-ketoglutarate dependent dioxygenase; ALKBH5, alkB homolog 5; YTHDF2, YTH N6-Methyladenosine RNA Binding Protein 2; YTHDC1, YTH domain-containing protein 1.

Figure 3.. Regulation of cancer metabolism and tumour immunity by m⁶A in the tumour microenvironment.

(a) Cancer-intrinsic m⁶A methylation plays a critical role in modulating metabolism of 3 key nutrients: glucose, amino acid, and lipid. Cancer cells demonstrate aerobic glycolysis and primarily metabolize glucose to lactate as the end product. The m⁶A modifiers involved in regulation of glucose metabolism are listed in red. m⁶A also guides the metabolism of vital amino acids that are indispensable for tumour growth, and respectively implicated modifiers are listed for the metabolism of serine (yellow), glutamine (purple), and branched-chain amino acids (BCAAs) (green). Those modifiers engaged in cancer lipid metabolism are listed in brown. (b) Anti-tumour immunity is controlled by both cancer-intrinsic and immune cell-intrinsic m⁶A modifiers. Cancer-intrinsic modifiers (dark red) maintain PD-L1 expression and regulate functions of certain tumour-infiltrating immune cells. Immune cell-intrinsic modifiers regulating the functions of natural killer (NK) cell (blue), dendritic cell (DC) (orange), macrophage (purple), T cell (green), and regulatory T cell (Treg) (turquoise) are listed under the corresponding cells. METTL, methyltransferase; FTO, FTO alpha-ketoglutarate dependent dioxygenase; ALKBH5, alkB homolog 5, RNA demethylase; IGF2BP, insulin-like growth factor 2 mRNA-binding protein; YTHDF1/2, YTH N6-methyladenosine RNA binding protein 1/2; 3PG, 3-phosphoglycerate; 3PHP, 3-phosphohydroxypyruvate; 3PS, 3-phosphoserine; PHGDH, phosphoglycerate dehydrogenase; PSAT1, phosphoserine aminotransferase 1; SLC1A5, solute carrier family 1 member 5; BCAT1/2, branched chain amino acid transaminase 1/2; BCKA, branched-chain keto acids.

Figure 4.. Mechanisms underlying the dysregulation of m⁶A in cancer.

Genetic mutations and environmental factors act in different manners to affect three classes of m⁶A-related genes, m⁶A modulators, m⁶A modifiers and m⁶A mediators, and finally influence the abundance or function of m⁶A in carcinogenesis.

Figure 5.. Perspective schematics of m⁶A modification as assisting diagnostic, prognostic and drug predictive biomarkers in cancer patients.

m⁶A profile/signature as diagnostic markers for early detection and screening of cancer patients; as prognostic markers for assessment of patient prognosis (overall survival); as drug predictive marker to selection of cancer patients benefit from radio/chemo therapy, targeted therapy and immunotherapy. m6A modifiers in therapeutic resistance are listed. m6A modifiers promoting cancer treatment sensitivity are marked with green plus signs, indicating patients with certain level of indicated m⁶A modifier genes may benefit from indicated therapies; while m6A modifiers antagonizing cancer treatment are marked with red crosses, indicating patients with aberrant expressed indicated m⁶A modifier genes has low responds on indicated therapies. m⁶A profile/signature prediction model could be established by the global abundance of m⁶A, the gene mutation and expression signature of m⁶A associated modifiers (writers, erasers and readers), as well as gene signatures of a set of m⁶A modified non-coding RNAs, such as LncRNAs and miRNAs. METTL, methyltransferase; FTO, FTO alpha-ketoglutarate dependent dioxygenase; ALKBH5, alkB homolog 5, RNA demethylase. 5FU, 5 Fluorouracil.

Figure 6.. Small molecule inhibitors targeting m⁶A modifiers.

Small molecule inhibitors targeting FTO, METTL3 and IGF2BP2 are listed by timeline with chemical structures, half-maximal inhibitory concentration (IC₅₀) of enzymatic activity, and validated cancer types. FTOi, FTO inhibitors; METTL3i, METTL3 inhibitors; IGF2BP2, IGF2BP2 inhibitors. BC, Breast cancer; AML, Acute myeloid leukemia; GBM, Glioblastoma; PC, Pancreatic cancer; CC, Colon cancer; MN, Melanoma; GC, Gastric cancer; T-ALL, T-cell acute lymphoblastic leukemia.