CRISPR editing links an FTO variant to muscle insulin resistance

Genome-wide association studies have linked the at mass and obesity-associated (FTO) rs9939609-A allele to both obesity and leanness, but the underlying mechanisms remain unclear. To investigate this, CRISPR prime editing was used to introduce the rs9939609-A variant into human embryonic stem cells (hESCs) and differentiate them into multiple tissue types.

By: Gorm Palmgren - Mar. 10, 2025

The researchers generated isogenic cell lines differing only at this SNP and directed their differentiation into mesodermal, endodermal, and neuroectodermal progenitors (see Figure 1). Among the five tested lineages, skeletal muscle cells exhibited the most pronounced effects, with increased proliferation, differentiation, and metabolic ageing.

Figure 1. A schematic diagram illustrating the workflow utilising CRISPR-Cas9-based prime editing of... — Figure 1. A schematic diagram illustrating the workflow utilising CRISPR-Cas9-based prime editing of hESCs to study the effects of a specicific FTO SNP on cellular differentiation. Reproduced under the Creative Commons license from Figure 1A in Guang et al. (2024) Nature Communications, https://doi.org/10.1038/s41467-024-53820-2

Muscle progenitors carrying the rs9939609-A allele showed enhanced activation of the insulin/IGF signalling pathway, leading to initial increases in insulin sensitivity. However, long-term culture or exposure to a high-fat diet (HFD) resulted in the development of insulin resistance. This transition was visualised using a FoxO1-GFP reporter system, which tracks insulin signalling by monitoring the localisation of the FoxO1 protein.

In insulin-sensitive cells, FoxO1 remains in the cytoplasm, but in FTO rs9939609-A myotubes exposed to HFD serum, FoxO1 progressively translocated to the nucleus, indicating insulin resistance (see Figure 2). This shift was accompanied by decreased phosphorylation of key insulin pathway proteins, confirming a loss of insulin responsiveness.

Figure 2. Representative images of FoxO1-GFP-infected FTOrs9939609-TT-myocytes and... — Figure 2. Representative images of FoxO1-GFP-infected FTOrs9939609-TT-myocytes and FTOrs9939609-A-myocytes exposed to 1% HFD serum at day 0 and day 14. Scale bars, 200 μm. Reproduced under the Creative Commons license from Figure 4B in Guang et al. (2024) Nature Communications, https://doi.org/10.1038/s41467-024-53820-2

The study demonstrates that the FTO rs9939609-A allele enhances insulin and IGF signalling by increasing FTO expression and reducing m6A methylation on H19 lncRNA and IGF2 mRNA. CRISPR-edited muscle cells showed overactivation of the FTO-H19/IGF2 regulatory circuit, driving initial muscle growth and heightened insulin responsiveness but ultimately leading to insulin resistance with age or dietary stress.

By isolating the effects of a single genetic variant, this CRISPR-based approach clarifies how FTO polymorphisms influence muscle metabolism and their potential contribution to metabolic disease.

This research was led by Lu Guang and Ng Shyh-Chang at the Chinese Academy of Sciences, Beijing, and it was published in Nature Communications on Friday, 7 March 2025.

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