Abstract
Using mouse models and high-throughput proteomics, we conducted an in-depth analysis of the proteome changes induced in response to seven interventions known to increase mouse lifespan. This included two genetic mutations, a growth hormone receptor knockout (GHRKO mice) and a mutation in the Pit-1 locus (Snell dwarf mice), four drug treatments (rapamycin, acarbose, canagliflozin, and 17α-estradiol), and caloric restriction. Each of the interventions studied induced variable changes in the concentrations of proteins across liver, kidney, and gastrocnemius muscle tissue samples, with the strongest responses in the liver and limited concordance in protein responses across tissues. To the extent that these interventions promote longevity through common biological mechanisms, we anticipated that proteins associated with longevity could be identified by characterizing shared responses across all or multiple interventions. Many of the proteome alterations induced by each intervention were distinct, potentially implicating a variety of biological pathways as being related to lifespan extension. While we found no protein that was affected similarly by every intervention, we identified a set of proteins that responded to multiple interventions. These proteins were functionally diverse but tended to be involved in peroxisomal oxidation and metabolism of fatty acids. These results provide candidate proteins and biological mechanisms related to enhancing longevity that can inform research on therapeutic approaches to promote healthy aging.
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Data availability
All sample analysis run order files, mass spectrometry dia-PASEF raw folders corresponding to mouse tissue experiments (.d), FASTA database used to generate the assay libraries (.fasta), mouse hybrid spectral assay library (.txt) and its DIALib-QC report (.tsv), and three unnormalized peptide quantitation data files (.csv) for each tissue have been deposited with the ProteomeXchange Consortium via the PRIDE partner repository [50, 51] with the data set identifier PXD040497 (http://www.ebi.ac.uk/pride). Code describing our statistical data analysis that can be used to reproduce our main results can be found at https://github.com/longevity-consortium/M005MouseLongevityPaper2023.
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Acknowledgements
We thank Kelly Crebs for excellent technical assistance.
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This work was funded in part by the National Institutes of Health grants, from the National Institute of General Medical Sciences R01 GM087221, the Office of the Director S10OD026936, the National Institute on Aging U19AG023122, and the National Science Foundation award 1920268.
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Supplementary information
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Supplemental Figure 1: (A) Venn diagram of the number of proteins detected in each tissue. (B) Dendrogram of similarity in protein abundances across all tissues. (PNG 108 kb)
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Supplemental Figure 2: (A-C) Scatterplots comparing mean protein abundances between liver and kidney (A), liver and muscle (B), and kidney and muscle (C) samples across mice of both sexes. (D-F) Scatterplot comparing mean protein abundances between female and male samples in liver (D), kidney (E), and muscle (F) tissues. (PNG 342 kb)
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Supplemental Figure 3: Variation in protein abundances explained by mouse background, sex, and longevity intervention for each quantified protein in liver (A), kidney (B), and muscle (C) tissues. Results from fitting a random effects model with intervention nested within background for each protein individually. (D) The abundances by intervention and sex of proteins for which the percent variation explained by intervention was greater than 60% in liver samples. (PNG 746 kb)
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Supplemental Figure 4: The log2 fold-change and log10 Bayes factor for proteins within each treatment compared to controls for male (A) and female (B) kidney samples. Dashed vertical lines correspond to a log2 fold-change of +/- 0.5 while the dashed vertical line corresponds to a Bayes factor of 10. (PNG 569 kb)
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Supplemental Figure 5: The log2 fold-change and log10 Bayes factor for proteins within each treatment compared to controls for male (A) and female (B) muscle samples. Dashed vertical lines correspond to a log2 fold-change of +/- 0.5 while the dashed vertical line corresponds to a Bayes factor of 10. (PNG 464 kb)
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Supplemental Figure 6: Fold-changes in response to each longevity intervention in females (x-axis) compared to males (y-axis) in liver (A), kidney (B), and muscle (C) tissues. Dashed lines indicate log2 fold-changes of +/- 0.5 in males (horizontal) and females (vertical), while the diagonal dotted line marks a 1:1 relationship. Points are colored blue if the protein exhibited an absolute log2 fold-change greater than 0.5 with a Bayes factor greater than 10 in both sexes, red if in males only, yellow if in females only, and grey if in neither. (PNG 1040 kb)
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Supplemental Figure 7: (A) Changes in protein abundances across multiple longevity treatments in kidney. Proteins shown are limited to those exhibiting an absolute log2 fold-change ≥ 0.5 and a Bayes factor ≥ 10 in response to at least three interventions of either sex. The color of the points indicates the associated Bayes factor and the size is proportional to the magnitude of the fold-change with closed points indicating a positive change and open points indicating a negative change. (B) GO-Terms that are enriched (with an associated adjusted p-value ≤ 0.01) among proteins with shared responses across longevity promoting interventions in kidney. (PNG 1022 kb)
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Supplemental Figure 8: Changes in protein abundances across multiple longevity treatments in muscle. Proteins shown are limited to those exhibiting an absolute log2 fold-change greater than ≥ 0.5 and a Bayes factor ≥ 10 in response to at least three interventions of either sex. The color of the points indicates the associated Bayes factor and the size is correlated with the magnitude of the fold-change with closed points indicating a positive change and open points indicating a negative change. No GO-Terms where are enriched with an associated adjusted p-value ≤ 0.01 among proteins with shared responses across longevity promoting interventions in muscle. (PNG 218 kb)
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Supplemental Figure 9: Comparison of protein responses to longevity interventions in mouse livers to protein differences between long-lived humans and not in the MrOS study for proteins detected in both datasets for liver, kidney, and muscle tissues. The color of the points indicates the associated Bayes factor and the size is proportional to the magnitude of the fold-change with closed points indicating a positive change and open points indicating a negative change. (PNG 1008 kb)
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Supplemental Figure 10: Protein responses to longevity-promoting intervention-by-sex groups in mouse liver, kidney, and muscle for proteins also differentially abundant in centenarians in NECS. Proteins shown are limited to those that exhibit both differential abundance in centenarian humans compared to controls with an adjusted p-value less than 0.001 in NECS and exhibited an absolute log2 fold-change ≥ 0.5 and a Bayes factor ≥ 10 in response to at least one interventions of either sex in mice. The color of the points indicates the associated Bayes factor and the size is proportional to the magnitude of the fold-change with closed points indicating a positive change and open points indicating a negative change. (PNG 1382 kb)
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Burns, A.R., Wiedrick, J., Feryn, A. et al. Proteomic changes induced by longevity-promoting interventions in mice. GeroScience 46, 1543–1560 (2024). https://doi.org/10.1007/s11357-023-00917-z
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DOI: https://doi.org/10.1007/s11357-023-00917-z