Protein restriction reprograms the multi-organ proteomic landscape of mouse aging

Aging is a major risk for life-threatening diseases. In recent years, protein restriction (PR) has gained recognition as a viable and practical intervention for promoting healthy aging. However, considering the complexity of aging and the importance of assessing the effectiveness and safety of PR prior to implementation, it is essential to delve into the molecular alterations occurring in different organs.

While several extensive transcriptomics studies on aging covering five to 23 organs have been conducted, the need for proteomics studies remains crucial due to the limited correlation between transcripts and proteins. However, the existing proteomic investigations have primarily focused on no more than ten organs at just two time points, excluding vital organs including the adrenal glands, lymph nodes, and reproductive organs. Additionally, the two-time-point approach may introduce biases by confounding the effects of aging with those of diseases. Moreover, the impact of PR on multiple organs and the optimal timeframe for intervention remain largely unexplored.

To address these gaps, we conducted an extensive study involving the collection of 41 mouse organs at eight distinct time points spanning the mouse lifespan and implemented a dietary intervention with varying protein intake for different age and sex groups. We also obtained plasma samples from both mice and humans to investigate the systemic effects of aging and PR. We applied Pulse Data-Independent Acquisition (PulseDIA) for analyzing all 2,565 tissue samples and Tandem Mass Tag (TMT) for the 592 depleted plasma samples.

We observed tissue-specific expression patterns of aging hallmarks and identified 36 proteins that consistently changed across multiple organs, with immunoglobulins and serpins demonstrating particular significance. Notably, many of these changes started prior to maturation. PR mitigate age-related molecular changes in a tissue-specific manner, including epigenomic modifications in the urinary system and protein phosphorylation alterations in brown adipose tissue, brain, and seminal vesicle. Our findings were supported by Reduced-representation bisulfite sequencing, phosphoproteomics, and staining experiments. These molecular changes indicated improved health conditions under PR, such as reduced cancer risks in the bladder and enhanced adipose function through increased thermogenesis. Importantly, initiating PR during middle age yielded the most profound effects. Furthermore, our analysis of human and mouse plasma proteomic data indicated improved cardiovascular health under PR, although extreme low protein intake showed signs of increased inflammation.

In summary, our study provides the most comprehensive molecular insights to date regarding aging and PR effects in multiple organs. This work expands our understanding of PR as a geroprotective intervention, highlights the potential benefits and risks, and identifies the optimal time frame for PR interventions.