Machine learning-based predictions of dietary restriction associations across ageing-related genes

Background Dietary restriction (DR) is the most studied pro-longevity intervention; however, a complete understanding of its underlying mechanisms remains elusive, and new research directions may emerge from the identification of novel DR-related genes and DR-related genetic features. Results This work used a Machine Learning (ML) approach to classify ageing-related genes as DR-related or NotDR-related using 9 different types of predictive features: PathDIP pathways, two types of features based on KEGG pathways, two types of Protein–Protein Interactions (PPI) features, Gene Ontology (GO) terms, Genotype Tissue Expression (GTEx) expression features, GeneFriends co-expression features and protein sequence descriptors. Our findings suggested that features biased towards curated knowledge (i.e. GO terms and biological pathways), had the greatest predictive power, while unbiased features (mainly gene expression and co-expression data) have the least predictive power. Moreover, a combination of all the feature types diminished the predictive power compared to predictions based on curated knowledge. Feature importance analysis on the two most predictive classifiers mostly corroborated existing knowledge and supported recent findings linking DR to the Nuclear Factor Erythroid 2-Related Factor 2 (NRF2) signalling pathway and G protein-coupled receptors (GPCR). We then used the two strongest combinations of feature type and ML algorithm to predict DR-relatedness among ageing-related genes currently lacking DR-related annotations in the data, resulting in a set of promising candidate DR-related genes (GOT2, GOT1, TSC1, CTH, GCLM, IRS2 and SESN2) whose predicted DR-relatedness remain to be validated in future wet-lab experiments. Conclusions This work demonstrated the strong potential of ML-based techniques to identify DR-associated features as our findings are consistent with literature and recent discoveries. Although the inference of new DR-related mechanistic findings based solely on GO terms and biological pathways was limited due to their knowledge-driven nature, the predictive power of these two features types remained useful as it allowed inferring new promising candidate DR-related genes.

Endogenous DAF-16 Spatiotemporal Activity Quantitatively Predicts Lifespan Extension Induced by Dietary Restriction

In many organisms, dietary restriction (DR) leads to lifespan extension through the activation of cell protection and pro-longevity gene expression programs. In the nematode C. elegans, the DAF-16 transcription factor is a key aging regulator that governs the Insulin/IGF-1 signaling pathway and undergoes translocation from the cytoplasm to the nucleus of cells when animals are exposed to food limitation. In this work, we assess the endogenous activity of DAF-16 under various DR regimes by coupling CRISPR/Cas9-enabled fluorescent tagging of DAF-16 with quantitative image analysis and machine learning. Our results indicate that lifelong DAF-16 endogenous activity is a robust predictor of mean lifespan in C. elegans, and it accounts for 78% of the lifespan variability induced by DR. We found that this lifespan-extending mechanism occurs mainly in the intestine and neurons, and that DR drives DAF-16 activity in unexpected locations such as the germline and intestinal nucleoli.

New Directions in Dietary Restriction: Remembering Edward Masoro

In 1935, Clive McCay reported that severe restriction of food increased the lifespan of male rats. In the following four decades, several laboratories replicated this observation with less sever restrictions, which will be referred to as dietary restriction (DR). However, there were concerns even in the aging community in the 1970s as to whether DR increased lifespan by retarding aging. It was the research of two former Kleemeier Awardees, Edward Masoro and Roy Walford, that conclusively demonstrated in the 1980s that DR retarded aging resulting in improved healthspan and reduced pathology. Ed Masoro’s research was focused on lipid metabolism when he was invited to attend a workshop on metabolism and aging in 1969. His interest in aging was piqued such that the more he learned about aging, the more interested he became. In a subsequent workshop in 1973, Ed heard Morris Ross describe his research on restricting food intake on cancer and longevity. Ed was impressed that a relatively simple manipulation had such dramatic effects, and he decided to focus his research on DR. After an extensive review of the DR literature up to the 1970s, Ed established the 40% restriction paradigm, which is used in almost all DR studies to date. Ed’s group was the first to study aging and DR under barrier conditions which he established at San Antonio. Over the next two decades, Ed would direct a Program Project that showed DR had a dramatic effect on most age-related pathologies and improved many physiological functions. Studying the restriction of fat, protein, micronutrients, Ed came to the conclusion that total calories consumed was a key factor in the effect of DR on longevity. His group was the first to show that DR significantly reduced circulating levels of glucose and insulin, which was subsequently shown to occur because of increased insulin sensitivity and is now recognized as a hallmark of DR and potentially important in the anti-aging action of DR. Ed was chair of the Biological Sciences Section of GSA in 1979 and President in 1995. This session is dedicated to Edward Masoro who passed away on July 11, 2020 at the age or 95.Dr. Masoro was president in 1995 and BS chair in 1979, Clive McCay was President in 1949.

Ribosomal Protein 6 Phosphorylation Regulates Translational Responses to Dietary Restriction

Forms of dietary restriction like intermittent fasting (IF) and caloric restriction (CR) promote health and longevity through changes in gene expression. While the transcriptional changes that occur in response to DR have been well described across several species, the role of translational regulation has lagged. Using polysome profiling and mRNA-seq, we quantified changes in actively translated mRNAs that occur in C. elegans under CR compared to well-fed conditions. The analysis revealed hundreds of transcripts regulated on the translational level that would have been missed using conventual transcriptomics. Among the translationally down-regulated genes that where pro-longevity when knocked down were regulators of the cell-cycle: fbxb-24, sdz-33, kbp-1, and cdk-2. In search of the mechanisms regulating selective translation under CR we investigated a role for ribosomal protein 6 (RPS-6) as its phosphorylation status is thought to regulate cell cycle and selective translation of mRNA transcripts. Using RPS-6 phospho-null and phospho-mimetic mutants, we show that phosphorylation and de-phosphorylation of RPS-6 is necessary for the pro-longevity effects of CR and IF. Furthermore, we show that IF is more beneficial for retaining locomotion with age than CR and that endogenously tagged RPS-6 ::mCherry accumulates in body wall muscle under fasting. However, the benefit of IF on locomotion is lost in RPS-6 phospho-mimetic mutants. Together, results suggest that protein translation is enhanced in the muscle under IF to prevent sarcopenia in a way dependent on RPS-6. Translatome analysis of the phospho-mutant suggested a role for RPS-6 in selective translation of p38 mitogen-activated protein kinases.

The Impact of Short-Term Dietary Restriction on Stem Cell Function

Stem cells play a critical role in the maintenance of tissue function and their proliferative/regenerative capacity is essential to this role. Because stem cells persist over the lifespan of an animal, they are susceptible to gradual accumulation of age-associated damage, resulting in the loss of regenerative function that can impair organ function. Understanding the mechanism(s) that regulates stem cell function is essential for retarding the aging process, and stem cells are attractive targets for aging interventions. Dietary restriction (DR), the most robust anti-aging intervention to-date, has been shown to enhance the activity and integrity of stem cells in a variety of tissues (e.g., muscle, bone marrow, and intestine), and it is believed that effect of DR on stem cells plays an important role in the anti-aging action of DR. For example, DR has been shown to preserve and increase the number of intestinal stem cells (ISCs) and enhance their regenerative capacity in young animals. Data from my lab shows that ISCs from old mice have limited proliferation activity and form few if any organoids in vitro (a surrogate for a fully functional crypt) and that ISCs isolated from old mice on life-long DR show an improved ability to form organoids. While it is well accepted that life-long DR increases lifespan and has anti-aging effects an important aspect of DR that has been largely overlooked is that DR implemented only for a short time early in life can increase lifespan of rodents even when rodents are fed ad libitum the remainder of their life. In line with this, we recently found that ISCs from old mice fed DR for only a short-period resulted in a dramatic increase in ability of the ISCs to form organoids. This is the first evidence that short-term DR administrated late in life can rescue the loss in ISC function that occurs with age.

Age-Related Neuroprotection by Dietary Restriction Requires OXR1-Mediated Retromer Function

Dietary restriction (DR) is the most robust method to delay aging and the onset of neurogenerative disorders across multiple species, though the mechanisms behind this phenomenon remain unknown. To elucidate how DR mediates lifespan extension, we analyzed natural genetic variants that associate with increased longevity under DR conditions in the Drosophila Genetic Reference Panel. We found that neuronal expression of the fly homolog of human Oxidation Resistance 1 (OXR1) is necessary for DR-mediated lifespan extension. Neuronal knockdown of OXR1 also accelerated visual decline but not physical decline, arguing for a specific role of OXR1 in neuronal signaling. Further, we find that overexpression of the TLDc domain from human OXR1 is sufficient for lifespan extension in a diet-dependent manner. Studies from the Accelerating Medicines Partnership - Alzheimer's Disease network show that patients with reduced OXR1 protein levels are more prone to Alzheimer's disease diagnosis, and we find that overexpression of human OXR1 is protective in animal and cell Alzheimer's models. In seeking the mechanism by which OXR1 protects against age-related neuronal decline, we discovered that it provides a necessary function in regulating the neuronal retromer complex, which is essential for the recycling of transmembrane receptors and for maintenance of autophagy. We further discovered that OXR1 deficiency can be rescued by genetic or pharmacological enhancement of retromer function, and that this enhancement extends lifespan and healthspan. Understanding how OXR1 operates could help uncover novel mechanisms to slow neurodegeneration including Alzheimer's disease.