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 an organism responds to nutrient status to 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 various organs and the microbiome communicate with each other to influence various physiological processes. We study how various physiological and molecular processes including physical activity, fat metabolism, circadian clocks, advanced glycation end products, calcification and intestinal permeability are influenced by nutrients to impact organismal health and survival. Our work has relevance to a number of age-related human diseases including diabetes, kidney stone formation, intestinal diseases, cancer and obesity. Some of the projects currently being pursued in the lab are described below.

Lab philosophy. Creativity and Collaboration’ We aim to utilize creative approaches to understand the mechanisms by which nutrients influence cellular homeostasis and disease processes. We also strive to develop models for various human diseases that are influenced by nutrient status using invertebrates. We collaborate with multiple groups to undertake interdisciplinary approaches to translate our findings from multiple models including, Drs. Marshall Stoller, Rachel Brem, Judith Campisi, Gordon Lithgow, Simon Melov, Julie Andersen, Arvind Ramanathan, Brad Gibson, Henri Jasper and Richmond Sarpong, 

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 previously demonstrated that modulation of mRNA translation is a key output of the TOR pathway that mediates DR responses on metabolism and lifespan. We have now established a ribotag based method in D. melanogaster to study tissue-specific mRNA translation. Tissue-specific mRNAs are 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, showing a highly tissue specific response upon DR. 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, which mediates the lifespan extension upon DR. We also hypothesize that the DR mediated increase in mitochondrial function, is part of a metabolic switch that enhances fatty acid metabolism. 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 in DR mediates changes in metabolism we are identifying and characterizing various tissue specific modulators of fat metabolsm 

and spontaneous activity. 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. We are understanding the mechanisms that modulate stone formation and translate our findings to human diseases like gout and cystinuria.

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. Our preliminary data demonstrates that DR enhances the amplitude of circadian genes and may inhibit the age-relate decline in loss of circadian homeostasis. We have identified a critical requirement for body clocks in modulating fat metabolism and lifespan upon dietary restriction. We are examining how nutrients modulate changes in clock function in various tissues. Furthermore, we are examining the role of various circadian clock components in modulating lifespan in response to nutrient variation in the diet. 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'.

Modelling the effect of nutrients on diabetic complications using C. elegans. As patients suffering from diabetes mellitus age, they often develop diabetic complications, such as neuropathic pain, renal failure, heart disease, blindness, and neurodegenerative disorders, almost doubling the risk of death. Persistent hyperglycemia in diabetes mellitus results in an accumulation of a series of reactive α-dicarbonyl compounds (α-DCs, e.g. glyoxal/GO, methylglyoxal/MGO, 3-deoxyglucosone/3DG) and α-DC-derived metabolites, called advanced glycation end products (AGEs). A major bottleneck in understanding the biochemistry behind the progression of these complications, and hence rapid drug development, is the lack of genetically tractable models that can recapitulate the effects of α-DC and AGE accumulation in a short time frame. To that end, we have established a Caenorhabditis elegans model to study the effects of nutrients on α-DC and AGE-related pathologies. These animals exhibit several phenotypes reminiscent of diabetic complications, such as accumulation of MGO and AGEs, hyperesthesia (or hyper sensitivity to touch), neuronal damage, within two weeks of adulthood. Using this model we have identified a critical pathway and novel pharmacological compounds that can ameliorate AGE-related pathologies in C. elegans. Together these aims will help to decipher the α-DC detoxification network and identify therapeutic targets and novel compounds that can mitigate diabetic complications and extend healthspan of diabetics.
Phone: 415-209-2201
Administrative Lab Coordinator: Molly Susag
Phone: 415-209-2084

“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



Recent Publications


David W Killilea, Jodi L Westropp... Marshall L Stoller "Elemental Content of Calcium Oxalate Stones from a Canine Model of Urinary Stone Disease." PLoS ONE 10:6 e0128374
Thomas Chi, Man Su Kim... Marshall L Stoller "A Drosophila model identifies a critical role for zinc in mineralization for kidney stone disease." PLoS ONE 10:5 e0124150
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