Researchers introduce SINGULAR, a cell rejuvenation atlas that provides a unified analysis framework to study the effects of rejuvenation strategies at the single-cell level.
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Researchers Javier Arcos Hodar, Sascha Jung, Mohamed Soudy, Sybille Barvaux, and Antonio del Sol from CIC bioGUNE-BRTA and University of Luxembourg introduce SINGULAR, a cell rejuvenation atlas that provides a unified analysis framework to study the effects of rejuvenation strategies at the single-cell level. On September 9, 2024, their 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 17, entitled, “The cell rejuvenation atlas: leveraging network biology to identify master regulators of rejuvenation strategies.”
THE RESEARCH
Various strategies, including lifestyle changes, gene therapies, and surgical procedures, have shown promise in improving aging markers and increasing lifespan in model organisms. These interventions often have limitations, however, such as not achieving comprehensive functional improvement across tissues or facing challenges in clinical translation. To address these limitations, the researchers characterized and compared rejuvenation interventions at different biological levels. The paper introduces SINGULAR, a cell rejuvenation atlas that provides a unified analysis framework to study the effects of rejuvenation strategies at the single-cell level. By examining gene regulatory networks, intracellular signaling, cell-cell communication, and cellular processes, the atlas identifies master regulators and common targets across immune cells. SINGULAR has the potential to inform future advancements in human age reversal and aid in the selection of drugs that mimic the effects of rejuvenation interventions.
RESULTS
The authors propose a unified multiscale analysis pipeline for characterizing and comparing the effects of rejuvenation interventions. This process begins by filtering low-quality cells, normalizing expression profiles, and identifying optimal cell clustering. The data is then analyzed at various biological levels, including differential gene expression, transcriptional regulatory networks, signaling cascades, and intercellular communication.
Nine previously published single-cell RNA-seq datasets from different rejuvenation interventions were collected and analyzed, revealing technical variability that highlights the need for a standardized data processing pipeline. The analysis showed heterogeneous gene expression responses across different cell types and organs. Systemic interventions had consistent effects on multiple organs, while metformin had minimal impact. Interestingly, exercise produced the largest transcriptional effects in the liver, artery, and spinal cord, even though it primarily targets muscles.
Transcriptional regulatory networks (TRNs) were reconstructed to explore the regulatory mechanisms behind these gene expression changes. The TRNs, which averaged 72 genes, were highly hierarchical, indicating the presence of ‘master regulators’ that explain significant portions of gene expression changes.
To demonstrate the practical application of SINGULAR, the study investigated the identification of drugs that could target transcription factor (TF) master regulators and key signaling molecules. Drug-target relationships from DrugBank were analyzed to find drugs that could activate master regulators or mimic the effects of rejuvenation interventions. Interestingly, only 17 out of 239 TFs could be activated by drugs, primarily nuclear receptors, with notable exceptions like AP-1 complex proteins and Trp53. Some of these drugs, such as Curcumin and Vitamin D3, have shown rejuvenating effects on lifespan in model organisms. Key signaling molecules were found to be more druggable, with several drugs targeting specific molecules, though none targeted both genes.
The study aimed to identify master regulators and their downstream effects in rejuvenation interventions. By simulating the activation of transcription factors (TFs) within the network, the researchers quantified the number of genes regulated by each TF. They discovered 493 TFs with non-zero activity across various conditions, though most acted as master regulators in only a few cases. The study also highlighted key differences between TFs involved in aging-related activity changes and those regulating rejuvenation. Notably, the AP-1 complex, consisting of Fos and Jun, emerged as a common master regulator across multiple interventions. The researchers also identified TFs linked to aging and validated their potential rejuvenating effects experimentally. They also explored crosstalk between TFs and signaling pathways, finding negative enrichment of aging gene sets in several integrated networks. Overall, the findings offer valuable insights into the regulatory mechanisms and potential rejuvenating effects of master regulators and signaling molecules involved in rejuvenation interventions.
CONCLUSION
In conclusion, this study employed a unified analysis pipeline, SINGULAR, to compare the effects and mediators of various rejuvenation interventions. Key master regulators, including Arntl, AP-1 complex proteins, NFE2L2, and MAF, were identified as playing crucial roles in rejuvenation. The analysis revealed distinct differences between aging-related transcriptional changes and rejuvenation regulators. Immune and skin cell types were highlighted as potential intervention targets, with the possibility of additive or synergistic effects by targeting non-overlapping master regulators. Some limitations were noted, such as biases in cell type comparisons, reliance on ligand-receptor interactions for cell-cell communication analysis, and the risk of false negatives in differential expression testing. Despite these limitations, SINGULAR offers valuable insights into rejuvenation mechanisms and the identification of agents for anti-aging strategies. It provides a robust framework for understanding the mechanisms behind various interventions and offers a wide range of potential target genes for a comprehensive anti-aging approach.
Click here to read the full research paper in Aging.
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Aging 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).
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