ATF4 activates a transcriptional program that chronically suppresses mTOR activity promoting neurodegeneration in Parkinson’s disease models
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Abstract
The Integrated Stress Response (ISR) is a cell signaling pathway that enables cells to adapt to diverse cellular stresses. Conversely, during chronic/unmitigated cellular stress the ISR becomes maladaptive and has been implicated in a range of neurodegenerative conditions including Parkinson’s Disease (PD). However, the mechanisms by which maladaptive ISR/ATF4 signaling contributes to neurodegeneration have not been elucidated. In this study we establish a critical mechanism by which chronic ISR activation becomes maladaptive and promotes neurodegeneration in neurotoxin and α- synucleinopathy models of PD in vitro and in vivo .
Specifically, we demonstrate that chronic activation of ATF4, the central transcription factor of the ISR, promotes neurodegeneration by regulating the transcriptional induction of SESN2, DDIT4 and Trib3 that co-operate to suppress both mTORC1 and mTORC2 activity. Furthermore, we demonstrate that ATF4-mediated suppression of mTORC1/2 activity promotes dopaminergic neuronal death in PD models by facilitating the activation of the pro- apoptotic BCL-2 family protein PUMA. Taken together, we have discovered a novel maladaptive ISR/ATF4 signaling pathway leading to chronic suppression of mTORC1/2 activity resulting in PUMA-mediated neuronal death that may have therapeutic implications in a range of neurodegenerative conditions that exhibit chronic ISR activation.
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This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/17992724.
Title of reviewed article: ATF4 activates a transcriptional program that chronically suppresses mTOR activity promoting neurodegeneration in Parkinson's disease models
doi: https://doi.org/10.1101/2025.06.09.658667
Summary: The authors investigated the mechanisms underlying the protective-to-toxic transition of integrated stress response (ISR) signaling in multiple chemical and genetic models of Parkinson's disease (PD) in C. elegans. Knockout of Atfs-1, the C. elegans homolog of ATF4, leads to increased survival in three distinct models of PD neurodegeneration, highlighting the role of prolonged ISR activation in neuronal death. Several mRNAs (Sesn2, Ddit4, Trib3) associated with mTOR …
This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/17992724.
Title of reviewed article: ATF4 activates a transcriptional program that chronically suppresses mTOR activity promoting neurodegeneration in Parkinson's disease models
doi: https://doi.org/10.1101/2025.06.09.658667
Summary: The authors investigated the mechanisms underlying the protective-to-toxic transition of integrated stress response (ISR) signaling in multiple chemical and genetic models of Parkinson's disease (PD) in C. elegans. Knockout of Atfs-1, the C. elegans homolog of ATF4, leads to increased survival in three distinct models of PD neurodegeneration, highlighting the role of prolonged ISR activation in neuronal death. Several mRNAs (Sesn2, Ddit4, Trib3) associated with mTOR suppression were found to be downregulated in ATF4 knockout mouse cortical neurons, suggesting a connection between ISR activation and suppression of the translation-promoting mTORC. The authors support this connection further by demonstrating that knockdown of each of the three ATF4 targets prevented mTORC activity while overexpression of all three had the opposite effect. Finally, they provide evidence that this neuronal death is mediated by the protein, PUMA.
Overall, these findings are interesting and provide insight into the crosstalk between two major pathways involved in maintaining cellular health. Moreover, it demonstrates a mechanism by which prolonged activation of the ISR becomes toxic in PD by downregulating mTOR function. The use of multiple orthogonal methods to demonstrate the interaction between the ISR, mTOR, and PUMA is a key strength of this manuscript. Minor changes to the organization of data accompanied by expanding the rationale and description of each experiment would greatly improve the readability of this article.
Major feedback:
1. In figure 2F, the authors highlight that the decreased phosphorylation of p-FOXO3a is reminiscent of PUMA upregulation that they observed in a previous report (doi: 10.1038/s41418-020-00688-6). Firstly, to determine whether this observation could indeed be due to PUMA upregulation following overexpression of ATF4, PUMA abundance could be assessed on this western blot. If PUMA is not upregulated, then inclusion of the PUMA-/- condition in this figure distracts from the interesting observation that ATF4 overexpression strongly suppresses mTOR function.
2. Throughout the article, the authors analyze immune-stained neurons and perform statistical analysis using individual cells as biological replicates, artificially increasing the power of the analysis. Instead, the authors may perform the statistical tests on the average values from cells from each replicate. This would better represent the variability between biological replicates rather than cell-to-cell variation within a single experiment.
Minor feedback:
1. The PUMA data from Figure 2 can be moved to Figure 6 for a more cohesive discussion of the involvement of PUMA in mediating cell death downstream of the ISR.
2. This article benefits from the use of multiple model organisms. The authors could aid in the interpretation of their data from these distinct systems by indicating from which organism (worm or mouse) cultures were performed.
3. In figure 2D, gene ontology analysis was performed to identify pathways that are enriched among all differentially expressed genes (DEGs). This analysis would be better interpreted if the authors performed it separately on upregulated and downregulated genes.
4. In Figure 6A, the last bar on the graph is labelled with "DDIT3," but it is unclear whether the authors overexpressed DDIT3, rather than DDIT4 as in the surrounding panels. It would be helpful to know whether DDIT3, rather than DDIT4, was overexpressed here. If so, it could benefit readers outside the field to provide additional rationale for why a different protein was overexpressed in this experiment.
5. Figure 6A and 6C have different gene/protein nomenclatures. To improve the flow between figures, consider keeping gene/protein nomenclature consistent.
Competing interests
The author declares that they have no competing interests.
Use of Artificial Intelligence (AI)
The author declares that they did not use generative AI to come up with new ideas for their review.
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This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/17993255.
Summary: The authors investigated the mechanisms underlying the protective-to-toxic transition of integrated stress response (ISR) signaling in multiple chemical and genetic models of Parkinson's disease (PD) in C. elegans. Knockout of Atfs-1, the C. elegans homolog of ATF4, leads to increased survival in three distinct models of PD neurodegeneration, highlighting the role of prolonged ISR activation in neuronal death. Several mRNAs (Sesn2, Ddit4, Trib3) associated with mTOR suppression were found to be downregulated in ATF4 knockout mouse cortical neurons, suggesting a connection between ISR activation and suppression of the translation-promoting mTORC. The authors support this connection …
This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/17993255.
Summary: The authors investigated the mechanisms underlying the protective-to-toxic transition of integrated stress response (ISR) signaling in multiple chemical and genetic models of Parkinson's disease (PD) in C. elegans. Knockout of Atfs-1, the C. elegans homolog of ATF4, leads to increased survival in three distinct models of PD neurodegeneration, highlighting the role of prolonged ISR activation in neuronal death. Several mRNAs (Sesn2, Ddit4, Trib3) associated with mTOR suppression were found to be downregulated in ATF4 knockout mouse cortical neurons, suggesting a connection between ISR activation and suppression of the translation-promoting mTORC. The authors support this connection further by demonstrating that knockdown of each of the three ATF4 targets prevented mTORC activity while overexpression of all three had the opposite effect. Finally, they provide evidence that this neuronal death is mediated by the protein, PUMA.
Overall, these findings are interesting and provide insight into the crosstalk between two major pathways involved in maintaining cellular health. Moreover, it demonstrates a mechanism by which prolonged activation of the ISR becomes toxic in PD by downregulating mTOR function. The use of multiple orthogonal methods to demonstrate the interaction between the ISR, mTOR, and PUMA is a key strength of this manuscript. Minor changes to the organization of data accompanied by expanding the rationale and description of each experiment would greatly improve the readability of this article.
Major feedback:
1. In figure 2F, the authors highlight that the decreased phosphorylation of p-FOXO3a is reminiscent of PUMA upregulation that they observed in a previous report (doi: 10.1038/s41418-020-00688-6). Firstly, to determine whether this observation could indeed be due to PUMA upregulation following overexpression of ATF4, PUMA abundance could be assessed on this western blot. If PUMA is not upregulated, then inclusion of the PUMA-/- condition in this figure distracts from the interesting observation that ATF4 overexpression strongly suppresses mTOR function.
2. Throughout the article, the authors analyze immune-stained neurons and perform statistical analysis using individual cells as biological replicates, artificially increasing the power of the analysis. Instead, the authors may perform the statistical tests on the average values from cells from each replicate. This would better represent the variability between biological replicates rather than cell-to-cell variation within a single experiment.
Minor feedback:
1. The PUMA data from Figure 2 can be moved to Figure 6 for a more cohesive discussion of the involvement of PUMA in mediating cell death downstream of the ISR.
2. This article benefits from the use of multiple model organisms. The authors could aid in the interpretation of their data from these distinct systems by indicating from which organism (worm or mouse) cultures were performed.
3. In figure 2D, gene ontology analysis was performed to identify pathways that are enriched among all differentially expressed genes (DEGs). This analysis would be better interpreted if the authors performed it separately on upregulated and downregulated genes.
4. In Figure 6A, the last bar on the graph is labelled with "DDIT3," but it is unclear whether the authors overexpressed DDIT3, rather than DDIT4 as in the surrounding panels. It would be helpful to know whether DDIT3, rather than DDIT4, was overexpressed here. If so, it could benefit readers outside the field to provide additional rationale for why a different protein was overexpressed in this experiment.
5. Figure 6A and 6C have different gene/protein nomenclatures. To improve the flow between figures, consider keeping gene/protein nomenclature consistent.
Competing interests
The authors declare that they have no competing interests.
Use of Artificial Intelligence (AI)
The authors declare that they did not use generative AI to come up with new ideas for their review.
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