Periodic Reporting for period 1 - FOX-mTN (Dissecting FOXO-mediated Transcription Noise to Stall Cellular Dysfunction in Ageing)
Reporting period: 2022-06-01 to 2024-05-31
Ageing is the result of accumulated cellular dysfunction and loss of tissue homeostasis, which culminates in age-related pathologies. Tissue homeostasis relies on the balance between cell removal, proliferation, and regeneration, which is disturbed during ageing, and is particularly important for the vascular endothelium. Previous research, conducted by our group and collaborators, has shed light on the indispensable role of FOXO1 in endothelial homeostasis. Dysregulation of FOXO1, either through its loss or overexpression, has been linked to vascular abnormalities such as overgrowth and rarefaction, leading to the emergence of vascular malformations in diverse tissues including the retina, skeletal muscle, and liver.
Conversely, the decline in cellular function observed during ageing can also stem from defects in quality control mechanisms, such as those governing gene expression. For instance, ageing is associated with an increase in transcriptional noise and the accumulation of aberrant RNA molecules. However, the extent and significance of this phenomenon in both healthy and aged tissues remain poorly understood, despite its potential impact on cellular fitness during ageing.
Our project adopted a multidisciplinary approach that integrates computational multi-omics analyses and genetic manipulation techniques in both human cells and mouse models. The primary objective was to gain fresh insights into the emergence of transcriptional noise, elucidate its dependence on FOXO dysregulation, and unravel its implications for cellular homeostasis. By unravelling these intricate relationships, our aim was to contribute to a deeper understanding of the molecular mechanisms underlying ageing-related cellular dysfunction, with special emphasis on vascular health, and pave the way for potential therapeutic interventions.
In parallel, we sought to enhance the computational biology field by providing training opportunities for students and young researchers in computational approaches. The field is rapidly evolving in terms of applications, breadth of scope and the extent of what can be accomplished. However, there is a big demand for bioinformatics skills in research, particularly in Portugal, even though many life scientists had no contact with programming languages. This effort will contribute to strengthening national and European cooperation, not only in the topics covered in this project but also in a variety of other fields where computational biology is required.
Conversely, the decline in cellular function observed during ageing can also stem from defects in quality control mechanisms, such as those governing gene expression. For instance, ageing is associated with an increase in transcriptional noise and the accumulation of aberrant RNA molecules. However, the extent and significance of this phenomenon in both healthy and aged tissues remain poorly understood, despite its potential impact on cellular fitness during ageing.
Our project adopted a multidisciplinary approach that integrates computational multi-omics analyses and genetic manipulation techniques in both human cells and mouse models. The primary objective was to gain fresh insights into the emergence of transcriptional noise, elucidate its dependence on FOXO dysregulation, and unravel its implications for cellular homeostasis. By unravelling these intricate relationships, our aim was to contribute to a deeper understanding of the molecular mechanisms underlying ageing-related cellular dysfunction, with special emphasis on vascular health, and pave the way for potential therapeutic interventions.
In parallel, we sought to enhance the computational biology field by providing training opportunities for students and young researchers in computational approaches. The field is rapidly evolving in terms of applications, breadth of scope and the extent of what can be accomplished. However, there is a big demand for bioinformatics skills in research, particularly in Portugal, even though many life scientists had no contact with programming languages. This effort will contribute to strengthening national and European cooperation, not only in the topics covered in this project but also in a variety of other fields where computational biology is required.
Our first aim was to uncover the prevalence of readthrough transcripts in healthy human tissues and elucidate the factors influencing their production. Transcription Readthrough (TRT) occurs when the transcription machinery fails to read stop signals, resulting in longer aberrant transcripts that may disrupt cellular function. This phenomenon is linked to stress responses, viral infections, and cancer, but their prevalence and functional impact in healthy conditions have remained largely unexplored. Here, we analyzed nearly 3000 transcriptome profiles from the Genotype-Tissue Expression (GTEx) project using established bioinformatics tools. We found that at least 30% of all protein-coding genes produce RT transcripts, regardless of the transcriptional levels of their host genes. We found associations between this phenomenon and inherent genomic features such as splicing efficiency, the presence of GC-rich sequences and enhancer-specific histones. This study sheds light on the prevalence, regulation, and potential functional impact of transcription readthrough in healthy human tissues, opening avenues to further explore its intricate molecular mechanisms and physiological significance.
Despite our efforts, we did not uncover any significant relationship between transcriptional noise and its reliance on FOXO dysregulation that carried biological significance. Nonetheless, we conducted a thorough analysis following specific deletion of FOXO1 in endothelial cells (ECs) to explore its role in modulating homeostasis and to uncover novel insights into the intricate mechanisms governing the FOXO1 regulatory network. We explored gene expression patterns, identified binding sites, and assessed the involvement of key transcription factors in the process to shed light on previously unexplored details. In parallel, we investigated a new potential role for FOXO1 in regulating a group of mTORC1 inhibitors, key regulators in governing cellular processes such as protein synthesis, metabolism, and cell growth. Our findings underscore its potential significance in vascular biology and open avenues for potential novel therapeutic strategies.
Despite our efforts, we did not uncover any significant relationship between transcriptional noise and its reliance on FOXO dysregulation that carried biological significance. Nonetheless, we conducted a thorough analysis following specific deletion of FOXO1 in endothelial cells (ECs) to explore its role in modulating homeostasis and to uncover novel insights into the intricate mechanisms governing the FOXO1 regulatory network. We explored gene expression patterns, identified binding sites, and assessed the involvement of key transcription factors in the process to shed light on previously unexplored details. In parallel, we investigated a new potential role for FOXO1 in regulating a group of mTORC1 inhibitors, key regulators in governing cellular processes such as protein synthesis, metabolism, and cell growth. Our findings underscore its potential significance in vascular biology and open avenues for potential novel therapeutic strategies.