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Uncomplexed-TSC1 deploys novel mTORC1-independent pathway to exacerbate the liver glycogen storage in TSC

Xiaoqiao Yue^1,2, Yanping Zhang^1,2, Na Zhao³

¹Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China.

Cell Death & Disease

|November 14, 2025

Abstract:

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder caused by inactivating mutations in TSC1 or TSC2 gene, leading to mTORC1 hyperactivation. However, mTORC1-independent mechanisms in this disorder remain poorly understood. In the study, excess glycogen storage was found in Tsc1^-/- cells, Tsc1^+/- and Tsc1^{c.2500-2503delAACA} mice, as well as in Tsc2^-/- cells, Tsc2^+/^- and Tsc2^c.1113delA mice, with more pronounced accumulation in models with TSC2 defects. Mechanistically, the deficiency of TSC1 or TSC2 gene caused redundant uncomplexed-TSC2 or TSC1 protein, respectively. Strikingly, only uncomplexed-TSC1 downregulated the histone demethylase KDM5A, which in turn increased H3K4me3 levels at the METTL3 promoter to enhance its expression. The upregulated m⁶A "writer" protein METTL3 cooperated with the "reader" protein IGF2BP2 to stabilize GYS2 mRNA, causing the upregulation of GYS2 resulting in the glycogen storage. Thus, our study uncovered a novel mTORC1 independent pathway (TSC1-KDM5A-METTL3-IGF2BP2-GYS2) that underlies the excess glycogen storage, and that synergy of mTORC1-dependent and independent pathways leads to the more pronounced glycogen storage with TSC2 defects compared to those with TSC1 defects, reflecting the more severer clinical phenotypes in TSC patients with TSC2 mutations. Importantly, the restoration of glycogen homeostasis and significant amelioration of liver lesion in TSC2 defect models after the combination treatment of pharmacological inhibitors targeting mTORC1 and METTL3, unveil a potential clinic intervention for TSC patients to whom mTORC1 inhibitors are less effective or even ineffective.

Insights

Tuberous sclerosis complex (TSC) involves excess glycogen storage via an mTORC1-independent pathway. Targeting METTL3 alongside mTORC1 shows potential for treating TSC patients unresponsive to current therapies.

Area of Science:

Genetics and Molecular Biology
Cellular Metabolism
Disease Mechanisms

Background:

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder linked to TSC1/TSC2 mutations and mTORC1 hyperactivation.
mTORC1-independent pathways contributing to TSC pathogenesis are not well understood.
Excess glycogen accumulation is a characteristic feature in TSC models.

Purpose of the Study:

To elucidate novel mTORC1-independent mechanisms driving glycogen storage in TSC.
To investigate the role of TSC1/TSC2 deficiency in glycogen metabolism.
To identify potential therapeutic targets for TSC, especially for patients with limited response to mTORC1 inhibitors.

Main Methods:

Utilized Tsc1/Tsc2 deficient cell lines and mouse models.
Analyzed protein interactions and gene expression related to glycogen synthesis.
Investigated the role of KDM5A, METTL3, IGF2BP2, and GYS2 in glycogen accumulation.
Assessed therapeutic efficacy of combined mTORC1 and METTL3 inhibition in vivo.

Main Results:

Demonstrated significant excess glycogen storage in TSC models, more pronounced in TSC2 defects.
Uncovered a novel mTORC1-independent pathway: TSC1-KDM5A-METTL3-IGF2BP2-GYS2, regulating glycogen synthesis.
Showcased that TSC1 deficiency downregulates KDM5A, leading to METTL3 upregulation and subsequent GYS2 stabilization and glycogen storage.
Confirmed that combined inhibition of mTORC1 and METTL3 ameliorated liver lesions and restored glycogen homeostasis in TSC2 deficient mice.

Conclusions:

Identified a novel mTORC1-independent pathway responsible for excess glycogen storage in TSC.
The synergy between mTORC1-dependent and independent pathways explains more severe phenotypes in TSC2 mutations.
Combination therapy targeting both mTORC1 and METTL3 offers a promising therapeutic strategy for TSC patients, particularly those with TSC2 mutations and limited response to mTORC1 inhibitors.

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