The Role of Aberrant N6‑Methyladenosine in Brain Disorders

Zhenqi Shi

Wuxi Big Bridge Academy, Wuxi, China

Keywords: m6A Methylation, Brain Disorders, Synaptic Plasticity.

Abstract: N6-methyladenosine (m6A) methylation, the central eukaryotic RNA epigenetic modification, dynamically

modulates RNA metabolism via the “writer-eraser-reader” network and influences neural development,

synaptic plasticity, and brain disease progression. METTL3 suppresses Sox2 mRNA degradation during

neural development to promote neuronal differentiation, while YTHDF2 mediates axon guidance gene

degradation to modulate neural circuit assembly; YTHDF1-mediated local translation of synaptic proteins is

learning and memory dependent. In illness, m6A imbalance is the basis of pathogenic mechanisms in

Alzheimer's disease, glioblastoma, and traumatic brain injury. m6A regulatory components are potential

prospects in preclinical models, but more investigations are desirable into multi-modification interaction

machinery and tool development.

1 INTRODUCTION

One of the major processes that control brain

function is RNA epigenetic modification. N6-

methyladenosine (m6A) modification is the most

prevalent epitranscriptomic marker, representing

80% of all RNA base methylation. In mammals, mA

methylates 0.1%-0.4% of all the adenine in the

transcriptome at any time (Wiener & Schwartz

2021). The "writing" methyltransferase

(METTL3/METTL14) complex, comprising the

METTL3 adaptor protein, WTAP, and other linked

proteins KIAA1429 and RBM15/15B, is deposited

onto mRNA in this dynamic modification. The

"reader" proteins (e.g., YTHDF 1, 2, 3) are proteins

that bind specifically to the "eraser" enzyme (FTO,

ALKBH5), which is responsible for removing the

modification. M6A is also involved in mRNA

stability, translation, splicing, and miRNA

processing. Based on the context, certain reader

proteins will detect the m6A marker and advance its

function. Furthermore, as m6A is a reversible

modification, it is possible that both labeled and

unlabeled mRNA can be washed away quickly so

that stringent and quick regulation of mRNA is

accessible. Recent research has revealed that

dynamic m6A imbalance is closely correlated with

the occurrence and development of a range of brain

diseases, and its mechanism is multi-level

regulation including pathological protein

aggregation, metabolic disorder, inflammatory

activation, and epitranscriptome reprogramming,

which opens a new idea for the molecular

mechanism of brain diseases.

m6A modification is involved in

neurodegenerative diseases with pathological

protein expression spatially and temporally

regulated. For instance, in the AD brain tissue,

decreased m6A demethylase FTO expression

increases the stability of the mRNA for the tau

protein and worsens the neurofibrillary tangle.

Concurrently, deletion of YTHDF1 suppresses the

translational efficiency of synaptic-related genes

such as BDNF and impairs cognitive ability. In PD

models, METTL3-catalyzed α-synuclein mRNA

methylation significantly increases translation level

and fosters Lewy body formation. In psychiatric

and neurodevelopmental disorders, brain function

is modulated by m6A by controlling the

differentiation of neural stem cells and synaptic

maturation. In the model of ASD, METTL3

knockout results in abnormal Notch pathway

activation, suppresses neuronal migration and

synaptic plasticity, and leads to social behavior

abnormality. Aberrant m6A modification in

hippocampus of depression patients suppresses

neurogenesis through disruption of the serotonin

signaling pathway, and FTO gene polymorphisms

can worsen mood disorders through disruption of

m6A homeostasis. Besides, m6A interaction with

Shi, Z.

The Role of Aberrant N6-Methyladenosine in Brain Disorders.

DOI: 10.5220/0014487100004933

Paper published under CC license (CC BY-NC-ND 4.0)

In Proceedings of the 1st International Conference on Biomedical Engineering and Food Science (BEFS 2025), pages 301-306

ISBN: 978-989-758-789-4

301

other RNA modifications (e.g., A-to-I editing) can

influence neurological function through

competitive regulation of RNA structure, but its

synergistic mechanism in brain disorders remains to

be explored.

In brain injury repair and tumor, the

bidirectional regulatory role of m6A reveals its

complexity. METTL3 is involved in glioblastoma

(GBM) tumor progression through increased

oncogene translation, including EGFR, and the

overexpression of FTO facilitates immune evasion

by suppressing immune checkpoint molecules like

PD-L1. In ischemic stroke models, YTHDF1

inhibits neuronal apoptosis by enhancing survival

protein translation (e.g., Hsp70), and m6A

dynamics imbalance could strengthen the release of

inflammatory mediators (e.g., IL-6), inducing

secondary injury.

2 THE MECHANISM OF M6A

METHYLATION

N6-methyladenosine (m6A) is the most prevalent

epigenetic mark in eukaryotic RNA, whose dynamic

regulation relies on the synergistic actions of

"writers," "erasers," "readers," and the "anti-readers"

suggested in recent years. These regulatory elements

are crucial to nervous system development, synaptic

plasticity, and brain disease through the precise

modulation of the level and activity of RNA

methylation modification.

2.1 Writer Complex

As an m6A-modified methyltransferase complex,

Writer catalyzes site-specific methylation of RNA

adenine N6 by multi-subunit synergy. With METTL3

as the catalytic core, the reaction of this complex is

SAM-dependent as the methyl group donor and is

specifically recognized by RRACH motifs (e.g.,

GGACU) (Shi et al. 2019). While catalytically

inactive, the METTL14 positively charged RNA-

binding surface significantly increases substrate

binding and optimizes methyl transfer efficiency by

supporting the stability of METTL3's conformation.

WTAP functions as a scaffold protein in addition to

positioning the complex in the nucleus, bringing in

cofactors like VIRMA to facilitate preferential 3'UTR

methylation (Zhao et al. 2020). As specifically noted,

the RBM15/15B subunit controls neural stem cell

differentiation fate by binding to U-rich sequences for

targeting non-coding RNAs (e.g., XIST), which

signifies the multi-dimensional role of Writer in

epigenetic programming (Zhu et al. 2020). In the

pathological condition, Writer's dynamic

dysregulation was highly heterogeneous:

glioblastoma overexpression of METTL3 enhanced

ribosomal loading efficiency by increasing the m6A

modification of EGFR mRNA and promoted tumor

invasion; Downregulation of METTL14 in

Alzheimer's disease reduces m6A levels of synapse-

related genes (e.g., Shank3), suppresses YTHDF1-

mediated translation, and promotes cognitive decline

(Zhao et al. 2020). Moreover, METTL3 and

METTL14 enrichment within neurons illustrates

dynamic methylation reactions in extrasynaptic areas,

outlining new knowledge of the hypothesized

regulation of synaptic plasticity (Zhu et al. 2020).

2.2 Erasers

m6A modification reversal is sustained by

demethylases FTO and ALKBH5, which control

RNA methylation homeostasis via different

mechanisms. FTO oxidatively degrades methyl

groups gradually and its function is regulated very

precisely by oxidative stress (i.e., inhibition of ROS)

and metabolic microenvironment (i.e., competitive

binding of α-ketoglutarate by succinic acid) (Shi et al.

2019). FTO not only localizes in the nucleus but also

in axons and dendrites, participates in dopaminergic

neurotransmission and axonal growth, and its genetic

defects can cause postnatal growth retardation and

neurological dysfunction in mice (Zhu et al. 2020).

Reduced FTO activity in Alzheimer's disease can

directly connect the disease's pathological process by

increasing BACE1 mRNA stability and promoting β-

amyloid production (Zhao et al. 2020). Conversely,

ALKBH5 utilizes a one-step direct demethylation

reaction that is catalytically inefficient and

exclusively nuclear plaque localized and unable to

target cytosolic mRNA. During hypoxia, HIF-1α

induces ALKBH5 and exacerbates cerebral ischemic

neuron apoptosis through stabilizing HIF-1α mRNA.

In glioma, PD-L1 mRNA demethylation by

ALKBH5 facilitates immune checkpoint molecular

expression and induces tumor immune escape (Zhao

et al. 2020). Substrate specificity of FTO and

ALKBH5 has been demonstrated to be strongly

dependent on RNA sequence context and the

recruitment of accessory proteins (e.g.,

proline/glutamine-rich splicing factors) and thus

embodies the complexity of the functional network of

Eraser (Shi et al. 2019).

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2.3 Readers and Anti-Readers

The biological m6A modification process was

ultimately accomplished through methylation signal

recognition by the reader and anti-reader antagonistic

regulation. The traditional reader protein YTHDC1

controls Mecp2 mRNA processing via RNA splicing

regulation, and its mutation results in a Rett

syndrome-like phenotype. Cytosolic YTHDF1

promotes translation of synaptic protein (e.g.,

PSD95) by binding eIF3 translation factors, whereas

YTHDF2 shields neurons from cerebral ischemia via

degradation of pro-apoptotic genes (e.g., Bim)

mRNAs with the CCR4-NOT complex (Shi et al.

2019, Zhao et al. 2020). Non-YTH domain readers,

e.g., IGF2BP family, are currently tumor targets of

treatment interacting with m6A-modified mRNAs

(MYC, SOX2) via the KH domain to suppress

miRNA-mediated decay and preserve glioma stem

cell stemness (Zhu et al. 2020). Anti-reader reverses

m6A activity by competitive binding or structural

interference: HNRNPC binds to the flanking U-rich

motif of m6A, blocks YTH protein recognition by

steric hindrance, and controls dendritic delivery of

Grin2b mRNA, the NMDA receptor subunit; Fragile

X mental retardation protein (FMRP) represses

translational activation of YTHDF1 by binding to

m6A-modified Shank1 mRNA, and loss causes

synaptic plasticity damage, indicating the crucial role

of anti-reader in neurodegenerative diseases (Zhao et

al. 2020). Furthermore, G3BP1/2 stabilizes the

transcript by being bound to un-methylated

CAACUC motif and creating an antagonistic

dynamic network with YTH protein and expanding

the coverage of m6A regulation (Shi et al. 2019).

3 THE NORMAL ROLE OF M6A

IN THE BRAIN

3.1 Neural Development and

Differentiation: Dynamic

Regulatory Network of m6A

m6A dynamically regulates the fate determination,

neuron differentiation, and region-specific

development of neural stem cells (NSCs) through

epitranscriptional regulation of RNA molecules (e.g.,

mRNA, lncRNA, miRNA). It is dependent on the

synergistic action of methyltransferase complexes

(METTL3/METTL14/WTAP), demethylases

(FTO/ALKBH5), and reading proteins

(YTHDF/YTHDC). FTO controls the lipid

metabolism microenvironment of NSCs in mouse

models by modulating the m6A levels of fat

generation-related genes (e.g., PPARγ). FTO

knockdown causes dyslipidemia production,

represses proliferation of NSCs, and initiates

astrocyte differentiation, eventually decreasing the

formation of neurons (Chen et al. 2019, Cao et al.

2020). METTL3 mediated m6A modification can

improve mRNA stability of key genes during

neurodifferentiation (e.g., NeuroD1 and Sox2), and

thus initiate the differentiation of NSCs into the

neural lineage. METTL3 inhibition initiates abnormal

over-piling of undifferentiated NSCs, and results in

abnormalities in cortical development (Livneh et al.

2020, Wei & He 2021, Yang et al. 2019). During

cerebellar development, METTL3 controls cell

migration and differentiation by interfering with the

Shh pathway-associated genes (like Gli1) of the

granule neuron precursors. METTL3 loss leads to a

reduction in the thickness of the cerebellar granule

layer, thereby affecting motor coordination (Livneh

et al. 2020, Zhang & Wang 2023). METTL14

deficiency impairs the spatiotemporal control of

radial neuron migration in the cerebral cortex,

causing impaired cortical stratification (e.g., lower

number of upper neurons), which is associated with

the dysregulation of m6A-dependent cell adhesion

molecules (e.g., Reelin) (Livneh et al. 2020, Zhang &

Wang 2023). Moreover, YTHDF2 controls the

accuracy of axon growth cone guidance by degrading

m6A-modified axon guidance mRNA (e.g., Ephrin

receptor). This failure of the mechanism could initiate

aberrant associations in the neuronal network (Zhang

& Wang 2023).

3.2 Synaptic Plasticity and Learning

Memory: Rapid Response and

Long-Term Regulation of m6A

m6A directly contributes to synaptic reorganization,

memory consolidation, and maintenance of cognitive

processes by dynamic control of the translational

efficacy and local stability of synaptic-related

mRNAs, in temporal and spatial and stimulus

responsiveness. In hippocampal neurons, YTHDF1

selectively recognizes m6A-tagged mRNA unique to

synaptic plasticity (e.g., PSD95, GluA1) to induce

local translation. YTHDF1 knockdown is highly

effective at reducing the stability of long-term

potentiation (LTP) and disrupting spatial memory

formation (Livneh et al. 2020, Zhang & Wang 2023).

m6A modification should also be of highly specific

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regulation of local protein synthesis within synapses

by recruiting RNA-binding proteins (e.g., HNRNP

family) or synthesizing synaptic-related mRNA (e.g.,

Arc, Camk2α) into dendritic or axonal terminals (Wei

& He 2021, Zhang & Wang 2023). During fear

conditioning experiments, the degree of hippocampal

neuronal m6A develops very quickly following

memory acquisition to facilitate memory

consolidation by stabilizing immediate-early gene

transcripts like c-Fos. Blocking methylation of m6A

will prevent memory from being consolidated in the

long term (Livneh et al. 2020, Zhang & Wang 2023).

Environmental factors (e.g., enriched environment)

can stimulate the increase in modification level of

m6A on synaptic proteins by activating the mTOR

signaling pathway for overexpression of METTL3.

Such dynamic regulation enables the neuron to

accommodate changes in requirements of synaptic

strengths in a versatile way (Wei & He 2021, Zhang

& Wang 2023). Downregulation of YTHDF1

expression in the hippocampus of cognitive deficit

and m6A dysregulation mice models of Alzheimer's

disease causes a decrease in the translation of

synaptic proteins (e.g., synaptotagmin) and is

implicated in synaptic and memory loss. Restoration

of m6A levels can restore synaptic function to a

certain extent (Livneh et al. 2020, Zhang & Wang

2023). Decreased activity of FTO in an aging brain

may lead to hyper-accumulation of m6A, silencing

neuroplasticity genes like BDNF. Activation of FTO

may be a novel approach toward the remediation of

age-associated memory disorders (Cao et al. 2020).

4 THE ROLE OF ABERRANT

M6A IN BRAIN DISEASES

4.1 Alzheimer’s Disease

m6A methylation is implicated in the pathological

process of AD (Alzheimer’s disease) through

modulation of RNA metabolism and protein

homeostasis. The pathological process of AD

includes accumulation of beta-amyloid protein (Aβ),

Tau protein abnormal phosphorylation, oxidative

stress, and damage to the cholinergic system (Shafik

et al. 2021, Yang et al. 2020, Xu et al. 2020).

Abnormal m6A modification was found to be highly

associated with neurodegenerative alterations in AD.

For instance, overexpression of METTL3 can result

in improper methylation of critical mRNAs and

influence synaptic plasticity and Aβ removal (Han et

al. 2020, Huang et al. 2020). Furthermore, dynamic

disequilibrium of m6A can induce mitochondrial

damage and oxidative stress and thus advance

neuronal apoptosis. Recent studies have also

indicated that Tau protein plays a protective function

by stabilizing microtubules in normal physiological

states but is controlled by m6A modification enzymes

under pathological phosphorylation, resulting in

neurofibrillary tangles (NFT), eventually causing

cognitive impairment (Huang et al. 2020).

Therapeutic strategies against m6A (e.g., inhibiting

METTL3 or activating demethylases) could become

potential therapeutic agents by controlling Aβ

metabolism and dynamic equilibrium of Tau protein.

4.2 Parkinson’s Disease

The pathological characteristics of PD (Parkinson’s

disease) include substantia nigra dopaminergic

neuron loss that is correlated with α-synuclein

accumulation and oxidative damage. m6A

modification plays a part in neuronal survival through

the regulation of antioxidant gene mRNA stability

(e.g., SOD2, GPX4) (Qin et al. 2020, Qiu et al. 2020).

Genome-wide association study identified that single

nucleotide polymorphisms of m6A-related genes

(like FTO, ALKBH5) are significantly related to the

risk of PD, and it indicated that m6A dysregulation

would enhance the progression of the disease via

mitochondrial dysfunction and neuroinflammation

(Qin et al. 2020, Qiu et al. 2020). Moreover, m6A

modification may also impact post-translational

modification of α-synuclein, but its exact mechanism

is to be investigated.

4.3 Other Brain Diseases

4.3.1 Brain Injury

Following brain injury, dynamic m6A regulation

plays a bivalent function in repair and

neuroinflammation. ALKBH5 and FTO play a role in

facilitated inflammatory responses by demethylating

pro-inflammatory mediators (e.g., TNF-α, IL-6)

mRNA, whereas METTL3 promotes neuronal

survival by triggering anti-apoptotic genes (e.g., Bcl-

2) (Xu et al. 2020). The process of oligodendrocyte

development and myelination depends on m6A

methylation, and METTL14 loss may lead to myelin

repair disease and exacerbate white matter injury (Xu

et al. 2020). Prior preclinical research has shown that

blocking the m6A modification enzymes (e.g.,

blocking ALKBH5 or activating METTL3) can

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improve the integrity of the blood-brain barrier and

promote neural regeneration, which provides new

ideas for the treatment of brain injury (Xu et al. 2020).

4.3.2 Brain Tumors

m6A methylation stimulates brain tumor growth

through the control of oncogene expression and

metabolic reprogramming. METTL3 and HNRNPC

are control proteins that facilitate the translation of

proto-oncogenes (e.g., MYC, EGFR) by m6A

modification and suppress the expression of tumor

suppressor genes (e.g., PTEN), increasing the

invasiveness of gliomas (Wang et al. 2020). The most

recent research discovery is that malignant gliomas

are capable of hijacking energy from neurons through

access to neural circuits, and m6A facilitates tumor

neuroinvasion through regulation of synaptic-related

genes (e.g., MMP-9). m6A reading protein IGF2BP2

also increases cancer cell chemoresistance by mRNA

stabilization of glutamine metabolism-related genes

(Wang et al. 2020). Small molecule m6A inhibitors

(e.g., FTO inhibitors) have been reported to be able to

inhibit tumor growth in preclinical models.

5 CONCLUSION

m6A methylation, the most common eukaryotic RNA

epimodification, is a master regulator of brain

disorders, neural development, and synaptic plasticity

by a dynamic regulatory network of "writers" (e.g.,

METTL3/METTL14 complex-catalyzed

methylation), "erasers" (e.g., FTO/ALKBH5-

mediated demethylation), "readers" (e.g., YTHDF1-

enhanced translation), and "anti-readers" (e.g.,

HNRNPC opposing recognition). In physiological

regulation, m6A facilitates neural formation by

stabilizing genes for neural differentiation (e.g.,

NeuroD1) and local synaptic translation control of

mRNA (e.g., PSD95) for secure learning and

memory; in pathology, m6A dysregulation creates

onset of disease: in Alzheimer's disease, m6A

hyperexpression or inhibition of FTO activity leads to

translational efficiency suppression in synaptic

proteins and deranged Aβ metabolism, in Parkinson's

disease, m6A gene polymorphism decides

antioxidant gene stability, in brain trauma, ALKBH5

promotes inflammation whereas METTL3 is

conducive to neuronal viability, and in gliomas,

METTL3/HNRNPC promotes invasiveness via

oncogenes (e.g., MYC). Interference with the m6A

regulatory pathway (for example, inhibition of

METTL3, activation of FTO, or blocking of

IGF2BP2) may well open up new avenues for

therapeutic intervention in neurodegenerative

disorders, brain injury, and cancer.

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