“Although transcriptomic changes are known to occur with age, the extent to which these are conserved across tissues is unclear.”
As we age, every tissue in the body undergoes gradual molecular changes. A long-standing question in aging research is whether these changes follow common patterns across tissues or whether each tissue ages on its own. While DNA-based “epigenetic clocks” can estimate age accurately across different tissues, identifying consistent patterns in gene expression has been much more challenging.
One reason for this difficulty is methodology. Most studies focus on whether genes increase or decrease their expression levels with age. However, genes do not function in isolation. They operate within complex networks, coordinating their activity with many others. Changes in these relationships may be important aspects of the aging process.
To understand this, researchers from the University of São Paulo performed a study titled “A combination of differential expression and network connectivity analyses identifies a common set of RNA splicing and processing genes altered with age across human tissues.”
The Study: Gene Expression and Network Analysis Integration to Study Aging Across Human Tissues
Featured on the cover of Aging-US (Volume 17, issue 12), the study analyzed gene expression data from nearly 1,000 donors from the Genotype-Tissue Expression (GTEx) project. They focused on 8 tissues (blood, brain, adipose tissue, muscle, blood vessel, heart, skin, and esophagus) from individuals aged 20 to 70.
Rather than relying only on traditional differential expression analysis, the team combined this approach with gene network analysis. This allowed them to check not only how strongly genes were expressed, but also how their patterns of coordination with other genes changed across aging. By integrating these two perspectives, the researchers aimed to capture age-related transcriptomic changes that might otherwise go undetected.
Results: Aging Alters Gene Networks and RNA Processing Across Human Tissues
The results revealed a clear and consistent pattern. Many genes showed little or no change in their average expression levels with age, yet their connectivity within gene networks changed substantially. In other words, aging often altered how genes interacted with one another rather than simply how active they were.
When gene expression and network connectivity were analyzed together, a core group of genes emerged as altered with age across nearly all studied tissues. These shared genes were not randomly distributed across biological functions. Instead, they were strongly enriched in processes related to RNA splicing and RNA processing, the steps that convert raw RNA transcripts into mature messages used to produce proteins.
These genes were also highly interconnected in protein–protein interaction networks, indicating that they function together as part of coordinated molecular systems. Many are components of known cellular complexes involved in RNA handling, suggesting that aging affects not just individual genes but entire functional groups.
Breakthrough: Network Analysis Reveals Hidden Conserved Aging Signatures Across Tissues
This study demonstrates that network-based analyses can uncover conserved aging-related changes that are largely invisible when analyzing gene expression alone. This approach helps explain why previous studies often failed to identify shared aging signatures across tissues.
Impact: Network Reorganization in RNA Processing Associated to Key Aging Mechanisms
Errors in RNA splicing can lead to the production of abnormal or malfunctioning proteins, which tend to accumulate as cells age. The study shows that tissues appear to respond to this by reorganizing networks involved in RNA processing, protein quality control, and degradation pathways such as autophagy. These coordinated changes align with well-known features of aging, including declining protein homeostasis.
Importantly, this network-based perspective helps reconcile conflicting findings in earlier research. Different tissues may show distinct gene-level changes, yet still be responding to the same underlying molecular stresses through different regulatory strategies.
Future Perspectives and Conclusion
This research highlights RNA splicing and processing as central and conserved features of transcriptomic aging across human tissues. It also underscores the importance of studying gene networks, rather than focusing exclusively on individual genes, when investigating complex biological processes such as aging.
While further work is needed to determine whether these changes actively drive aging or reflect adaptive responses to accumulating cellular damage, the findings offer a more integrated perspective on how aging develops at the molecular level. Ultimately, this knowledge may help guide strategies aimed at supporting healthier aging across multiple tissues rather than targeting isolated organs or pathways.
Click here to read the full research paper published in Aging-US.
___
Aging-US is indexed by PubMed/Medline (abbreviated as “Aging (Albany NY)”), PubMed Central, Web of Science: Science Citation Index Expanded (abbreviated as “Aging‐US” and listed in the Cell Biology and Geriatrics & Gerontology categories), Scopus (abbreviated as “Aging” and listed in the Cell Biology and Aging categories), Biological Abstracts, BIOSIS Previews, EMBASE, META (Chan Zuckerberg Initiative) (2018-2022), and Dimensions (Digital Science).
Click here to subscribe to Aging-US publication updates.
For media inquiries, please contact [email protected].