image: Figure 1. RNA-seq and proteomics were used to characterize cortical bone from young-adult and old mice at baseline. (A) Untreated 5-month-old (young-adult) and 22-month-old (old) female C57BL/6N mice were sacrificed. Paired right and left tibial mid-diaphyses were isolated, removed of marrow, and snap frozen. From the right tibias, proteins were extracted using 4% SDS. Proteins from 5 tibias per age were analyzed by proteomics using a tandem mass tag (TMT)-11. From the left tibias, RNA was isolated using TRIzol. RNA from 7 tibias per age was sequenced. (B) MicroCT of the distal right femurs from these mice confirmed the expected age-related differences in the cortical bone. (C, D) The distal cortical bone area and cortical thickness were lower with age. (E) MicroCT also confirmed age-related changes in the trabecular bone of the distal femur. (F, G) The bone volume per total volume (BV/TV) and trabecular number were lower with age. (H) Proteomics and RNA-seq raw data were analyzed, and differential expression analysis was performed separately. For both methods, a Benjamini-Hochberg-adjusted p-value cutoff of 0.05 was used to identify differentially expressed genes (DEGs) and differentially expressed proteins (DEPs). Downstream analyses included correlations, overlaps, weighted gene co-expression network analysis (WGCNA), gene ontology (GO) analysis, pathway analysis, and COMPBIO analysis. (I) 93% (1773/1904) of proteomics hits (PSM≥3) were detectable by RNA-seq (non-zero CPM for all samples). (J) The abundance of the 1773 targets detected by both proteomics and RNA-seq (after PSM and CPM filtering) were correlated (Spearman). (K) Comparing young-adult and old bone at baseline, 183 proteomics targets and 2290 RNA-seq targets met the p-value cutoff to be DEPs and DEGs, respectively. Abbreviations: SDS: Sodium dodecyl sulfate; BV/TV: Bone Volume/Total Volume; DEG: Differentially Expressed Gene; DEP: Differentially Expressed Protein; CPMs: Counts per million; PSMs: Peptide spectral matches.
Credit: 2024 Chermside-Scabbo et al.
“We conclude that proteomics is a promising approach to study bone biology and detect protein-specific changes in aging.”
BUFFALO, NY- October 15, 2024 – A new research paper was published on the cover of Aging (listed by MEDLINE/PubMed as "Aging (Albany NY)" and "Aging-US" by Web of Science), Volume 16, Issue 19 on October 12, 2024, entitled, “A proteomics approach to study mouse long bones: examining baseline differences and mechanical loading-induced bone formation in young-adult and old mice.”
As noted in the abstract, bone mass declines with age, and the anabolic effects of skeletal loading decrease. While much research has focused on gene transcription, how bone ages and loses its mechanoresponsiveness at the protein level remains unclear.
In their paper, researchers Christopher J. Chermside-Scabbo, John T. Shuster, Petra Erdmann-Gilmore, Eric Tycksen, Qiang Zhang, R. Reid Townsend, and Matthew J. Silva from Washington University School of Medicine and Washington University in St. Louis, Missouri, describe how they developed a novel proteomics approach and conducted paired mass spectrometry and RNA-seq analyses on tibias from young-adult (5-month) and old (22-month) mice.
The researchers report the first correlation estimate between the bone proteome and transcriptome (Spearman ρ = 0.40). While this is consistent with findings from other tissues, it suggests that only a relatively low amount of variation in protein levels is explained by variation in transcript levels.
Of the 71 shared targets that differed with age, eight were associated with bone mineral density in previous GWAS, including the understudied targets Asrgl1 and Timp2. Using complementary RNA in situ hybridization, the researchers confirmed that Asrgl1 and Timp2 showed reduced expression in osteoblasts/osteocytes in aged bones. Additionally, they found evidence of reduced TGF-beta signaling with aging, particularly Tgfb2. The researchers also identified proteomic changes following mechanical loading, noting that at the protein level, bone differed more with age than with loading, and aged bone exhibited fewer loading-induced changes.
"Overall, our findings underscore the need for complementary protein-level assays in skeletal biology research.”
Continue reading: DOI: https://doi.org/10.18632/aging.206131
Corresponding Author: Christopher J. Chermside-Scabboa - ccherms@wustl.edu
Keywords: aging, bone, mechanical loading, proteomics, RNA-seq/transcriptomics
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The journal Aging aims to promote 1) treatment of age-related diseases by slowing down aging, 2) validation of anti-aging drugs by treating age-related diseases, and 3) prevention of cancer by inhibiting aging. (Cancer and COVID-19 are age-related diseases.)
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Journal
Aging-US
Method of Research
News article
Subject of Research
Animals
Article Title
A proteomics approach to study mouse long bones: examining baseline differences and mechanical loading-induced bone formation in young-adult and old mice
Article Publication Date
12-Oct-2024
COI Statement
The authors declare no conflicts of interest related to this study.