Deep proteome profiling reveals signatures of age and sex differences in paw skin and sciatic nerve of naïve mice
Curation statements for this article:-
Curated by eLife
Evaluation Summary:
In addition to providing extensive proteomics profiling datasets. this manuscript is fundamental that sheds light on the importance of appropriate experimental design for mouse disease model which have been overlooked so far. The results look quite solid based on the proper methodology. This type of work is extremely valuable to many biomedical scientists in the field for conducting reproducible research especially in the preclinical studies and properly interpreting the results.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)
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Abstract
The age and sex of studied animals profoundly impact experimental outcomes in biomedical research. However, most preclinical studies in mice use a wide-spanning age range from 4 to 20 weeks and do not assess male and female mice in parallel. This raises concerns regarding reproducibility and neglects potentially relevant age and sex differences, which are largely unknown at the molecular level in naïve mice. Here, we employed an optimized quantitative proteomics workflow in order to deeply profile mouse paw skin and sciatic nerves (SCN) – two tissues implicated in nociception and pain as well as diseases linked to inflammation, injury, and demyelination. Remarkably, we uncovered significant differences when comparing male and female mice at adolescent (4 weeks) and adult (14 weeks) age. Our analysis deciphered protein subsets and networks that were correlated with the age and/or sex of mice. Notably, among these were proteins/biological pathways with known (patho)physiological relevance, e.g., homeostasis and epidermal signaling in skin, and, in SCN, multiple myelin proteins and regulators of neuronal development. Extensive comparisons with available databases revealed that various proteins associated with distinct skin diseases and pain exhibited significant abundance changes in dependence on age and/or sex. Taken together, our study uncovers hitherto unknown sex and age differences at the level of proteins and protein networks. Overall, we provide a unique proteome resource that facilitates mechanistic insights into somatosensory and skin biology, and integrates age and sex as biological variables – a prerequisite for successful preclinical studies in mouse disease models.
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Evaluation Summary:
In addition to providing extensive proteomics profiling datasets. this manuscript is fundamental that sheds light on the importance of appropriate experimental design for mouse disease model which have been overlooked so far. The results look quite solid based on the proper methodology. This type of work is extremely valuable to many biomedical scientists in the field for conducting reproducible research especially in the preclinical studies and properly interpreting the results.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)
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Reviewer #1 (Public Review):
Xian et al. systematically evaluated age and sex-dependent differences in paw skin and sciatic nerves (SCN) tissues of naïve mice, utilizing DIA-PASEF, a highly sensitive and reproducible proteomics approach. The authors demonstrated that the deep proteome profiling enabled a discovery of significant differences between male and female mice and adolescent and adult mice such as homeostasis and epidermal signaling in skin and, myelination and neuronal development in SCN that are known to be relevant to the pathophysiology. The authors claim the need for the appropriate age and sex matching in the experiment design and suggest the work as a unique systems biology proteome resource in mouse disease model. As I understand this is the first attempt to molecularly characterize the impact of mouse age and sex that …
Reviewer #1 (Public Review):
Xian et al. systematically evaluated age and sex-dependent differences in paw skin and sciatic nerves (SCN) tissues of naïve mice, utilizing DIA-PASEF, a highly sensitive and reproducible proteomics approach. The authors demonstrated that the deep proteome profiling enabled a discovery of significant differences between male and female mice and adolescent and adult mice such as homeostasis and epidermal signaling in skin and, myelination and neuronal development in SCN that are known to be relevant to the pathophysiology. The authors claim the need for the appropriate age and sex matching in the experiment design and suggest the work as a unique systems biology proteome resource in mouse disease model. As I understand this is the first attempt to molecularly characterize the impact of mouse age and sex that would help warrant the reproducibility of the preclinical research.
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Reviewer #2 (Public Review):
In this manuscript, the authors demonstrated age- and sex-dependent changes of proteome profiling of mouse paw skin and sciatic nerve (SCN) using two proteomic methods. Although there have been several reports showing transcriptome changes according to the age and sex, the current study provided proteome changes, which more reliably reflects the biological interpretations as the authors suggested. The results are interesting to understand age- and sex-dependent proteome changes in paw skin and SCN in association with disease-relevant functional pathways.
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Reviewer #3 (Public Review):
The paper emphasizes the importance of testing males and females in parallel when designing mice experiments as well as being consistent with age. In agreement with this, significant differences were observed between mice of different sexes and of varying ages. It also offers many insights into how DIA-PASEF workflows can improve performance in proteomics.
I would suggest to the authors they explain how experiments could be designed in a small scale in case there are time and financial constraints so that both female and male mice can be used simultaneously. It would also be beneficial to read over any challenges associated with the DIA-PASEF analysis. Enrich the discussion with performance comparison between DIA-PASEF and DDA-PASEF for mice proteomics data male versus female.
Were there any unique proteins …Reviewer #3 (Public Review):
The paper emphasizes the importance of testing males and females in parallel when designing mice experiments as well as being consistent with age. In agreement with this, significant differences were observed between mice of different sexes and of varying ages. It also offers many insights into how DIA-PASEF workflows can improve performance in proteomics.
I would suggest to the authors they explain how experiments could be designed in a small scale in case there are time and financial constraints so that both female and male mice can be used simultaneously. It would also be beneficial to read over any challenges associated with the DIA-PASEF analysis. Enrich the discussion with performance comparison between DIA-PASEF and DDA-PASEF for mice proteomics data male versus female.
Were there any unique proteins only found by DIA-PASEF? -
