Pankaj Kapahi, PhD, Professor

Understanding the role of nutrition and energy metabolism in lifespan and disease

Overall Goals. The overall goal of the Kapahi laboratory is to understand how different tissues orchestrate responses to nutrients to integrate physiological changes that influence health and disease. We utilize worms, flies and mice as model systems to understand how nutrients influence age-related changes in physiology and disease processes. Using interdisciplinary approaches we are examining the mechanisms by which tissues and the microbiome communicate with each other to influence various physiological processes, in response to nutrient variation, including physical activity, fat metabolism, calcification and intestinal permeability and organismal survival. This work has relevance to a number of age-related human diseases including intestinal diseases, obesity, cardiovascular diseases and insulin resistance.

Tissue specific architecture of nutrient dependent responses in D. melanogaster. The overall aim of this project is to examine the role of tissue-specific changes in mRNA translation in response to dietary restriction (DR) and to examine their role in modulating metabolism, muscle activity and healthspan using D. melanogaster. We have demonstrated that modulation of mRNA translation is a key output of the TOR pathway that mediates DR responses on metabolism and lifespan. We previously established a method to study genome-wide mRNA translation state in D. melanogaster. This method termed translation state array analysis (TSAA), assesses the mRNA translation state based on the separation of mRNAs bound to varying numbers of polysomes via density gradient centrifugation. However this approach fails to account for changes in multiple tissues. To overcome this we have established a ribotag based method in D. melanogaster to study tissue-specific mRNA translation. Tissue-specific mRNAs have been isolated following ribosome affinity purification of tissue-specific tagged ribosomal proteins followed by polysomal profiling. Using this ‘Ribotag’ approach tissue-specific changes under DR have been measured in muscle, fat, gut, heart, neurons, germline and malpighian tubules. We are developing mechanistic models of gene expression regulation and conducting comprehensive bioinformatics analyses on UTRs, promoters and the coding sequences of various elements of differentially regulated genes. Furthermore, we are testing candidate tissue specific genes using models described in the projects listed below to examine various nutrient responses including fat metabolism, physical activity, intestinal permeability, calcification and aging. These experiments will help dissect how nutrient changes orchestrates changes in multiple tissues to modulate age-related decline in various organismal and tissue-specific functions.

Understanding the link between fat metabolism, spontaneous activity and aging. We have previously demonstrated that DR increases both fat synthesis and breakdown, leading to an increase in fat turnover in the adult flies. We also hypothesize that the DR mediated increase in mitochondrial function, is part of a metabolic switch that enhances fatty acid metabolism. Increased fat metabolism is critical for the observed increase in activity upon DR. This was supported by our results that muscle specific inhibition of genes involved in triglyceride synthesis and breakdown, inhibits the increase in activity and healthspan observed upon DR. Furthermore, clipping or genetically ablating wings from flies prevented the protective effects of DR on lifespan, demonstrating a critical role for the observed increase in physical activity in determining lifespan upon DR. To further elucidate the mechanisms by which changes DR mediates changes in metabolism we are identifying and characterizing various tissue specific modulators of fat metabolism and spontaneous activity including 4E-BP upon nutrient manipulation. This has the potential to uncover pathways that may help counteract the deleterious effects of obesity and many age-related diseases by enhancing the activity and/or fat metabolism of the organism.

The role of nutrients in modulating gut function and permeability. Disruption of gut integrity is closely associated with longevity. We have observed that upon DR, flies show reduced gut permeability and higher tolerance to the pathogenic bacteria. The role of the gut, which is significantly altered upon dietary manipulation, remains poorly understood in DR. Our preliminary data suggests that changes in gut function and physiology in response to DR play a key role in modulating healthspan in Drosophila. In particular we are focusing on the impact of diet on intestinal barrier function and the associated innate immune responses to modulate healthspan. We have also identified a number of genes expressed in the gut whose changes with age are reversed by DR. We hypothesize that these subset of genes, whose expression is changed with age and reversed by DR, may help understand how DR reverses the age-related decline in gut function. Together these experiments will systematically examine and help understand the mechanisms by which DR modulates gut function and physiology and identify novel targets for therapeutic interventions which are likely to be relevant for human diseases where intestinal permeability has been observed (e.g. inflammatory bowel disease and HIV).

Nutrient dependent changes in calcification and mineralization. We have established genetic models for diet dependent changes in calcification in the fly malpighian tubules. These models allow genetic dissection of calcification which is to relevant to many diseases like atherosclerosis, gout, stone and bone formation. These calcification models also display remarkable similarity to kidney stones found in humans for which obesity is one of the biggest risk factor. We observe that inhibition of xanthine dehydrogenase (XDH) or uricase genes in D. melanogaster leads to significant increase in calcification on a nutrient rich diet which bears similarity to human randall plaques. Upon dietary restriction conditions almost no calcification is observed. Humans lost the uricase around 25 million years ago, and thus have elevated uric acid which is further elevated on a rich diet. Thus, inhibition of uricase recapitulates the human condition and our simple fly model maybe very useful in understanding the biological effects of altered uric acid. Uric acid elevation is associated with increased gout, diabetes and cardiovascular disease risk.

The role of circadian clocks in modulating nutrient responses.  Disruption of circadian clocks has been associated with accelerated aging and is a risk factor for many age-related diseases including cancer and diabetes. However, the underlying mechanisms remain poorly understood. Our preliminary data demonstrates cross-talk between circadian clocks and nutritional changes in in the diet that impact lifespan using D. melanogaster, on multiple levels. We are examining how nutrients modulate changes in clock function in various tissues. Furthermore, we are examining the role of circadian clocks in modulating lifespan in response to nutrient variation in the diet. Our previous data demonstrate that the protective effects of DR require a metabolic adaptation which necessitates a shift towards increased triglyceride turnover. Therefore, we are also examining the role of circadian clocks in modulating fat metabolism and its impact on aging. This work will initiate new awareness of circadian gene expression changes in aging and dietary restriction studies and contribute to the sub-discipline of 'chronogerontology'.

pkapahi@buckinstitute.org
Phone: 415-209-2201
Administrative Lab Coordinator: Ari Cohn
acohn@buckinstitute.org
Phone: 415-209-2229

“Our research will help us understand the molecular basis of the impact of nutrition on aging and age-related diseases in humans.’’

- Pankaj Kapahi, PhD

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