
The Ashrafi Lab studies energy balance in intact organisms using C. elegans as an experimental system investigating neural circuits regulating feeding behavior, neuroendocrine regulators of fat metabolism, and how metabolic state regulates behavioral plasticity. Additionally, the lab employs phenotypic screening and in silico predictions to identify and decipher the mechanisms through which small molecules affect fat and feeding mechanisms.
Regulation of fat content involves a complex interplay between central regulators of feeding behavior in the nervous system, neuroendocrine signals, and metabolic regulators of energy expenditure and fat storage. The lab uses genetic, cellular, and molecular approaches for understanding the networks that underlie the regulation of body fat in C. elegans. By combining classical mutagenesis screens with RNA-mediated interference to disrupt the expression of thousands of individual worm genes, Dr. Ashrafi's lab has identified over 500 genes that, when inactivated, affect body fat content in worms. These fat regulatory genes include receptors, channels, signal transduction molecules, transcription and translation factors, vesicular transporters, metabolic enzymes, and a number of genes with unassigned functions. The shared ancestry of the known mammalian and worm fat regulatory genes suggest that many of these newly identified genes may also function in human fat regulation.
The Ashrafi Lab seeks to:
- Understand molecular functions and regulatory modes of newly identified genes.
- Understand principles governing the networking of hundreds of genes expressed across multiple tissues regulating a complex physiological process.
- Delineate the neuronal networks that regulate food intake and energy expenditure in worms.
- Apply these findings to identify mammalian fat and obesity genes and analyze how gene misregulation results in obesity-associated diseases.
To decipher the modes of function of the newly identified genes, genetic interaction networks are established between various mutants and RNAi clones that cause fat reduction or fat increase. Suppressor/enhancer screens disentangle the complex feedback loops that affect body fat.
Fat regulatory genes can be broadly classified as those that impact food intake or energy expenditure. Thus, the lab measures each of these parameters in the mutant animals or animals exposed to each fat regulatory RNAi clone.
Fusion of GFP tags to fat regulatory proteins allows for monitoring cellular expression and subcellular localization of each of the fat regulatory genes. These GFP fusions classify the genes directly involved in fat storage and utilization or those that function as neuronal regulators of feeding and energy expenditure. These experiments categorize the RNAi clones into subsets with related functions. For example, kinases within a group would be likely to phosphorylate the metabolic enzymes or transcription factors of the same group. Moreover, it can be determined whether the expression or localization of a given fat regulatory gene is regulated by extrinsic or intrinsic signals such as fat levels, food, developmental stage, and other fat regulatory genes. Finally, since the complete map of the worm neuronal connections has been described, cellular localization of fat regulatory proteins could delineate the neuronal networks that regulate feeding behavior and energy expenditure. The lab tests the hypothesis using a combination of laser ablation of specific neurons and single neuron gene expression studies.
Importantly, these types of analyses can be applied to many C. elegans genes whose mammalian homologs have been implicated in diseases of fat and sterol metabolism. In collaborative studies, findings from C. elegans are being extended to rodent models of obesity. Genes discovered in C. elegans point to candidate obesity or diabetes loci within the large genomic regions identified in human pedigree and rodent studies. In other collaborative studies, candidate genes from collections of obese or diabetic pedigrees will be sequenced to identify variants.
Molecular and genetic analysis of newly identified fat regulatory genes including disease associated genes
Functional analysis of fat regulatory genes on food intake and energy expenditure
Identification of the neuronal networks that mediate energy homeostasis
Mapping and molecular cloning of fat regulatory mutants
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Neural production of kynurenic acid in Caenorhabditis elegans requires the AAT-1 transporter. Genes Dev. 2020 Aug 01; 34(15-16):1033-1038. Lin L, Lemieux GA, Enogieru OJ, Giacomini KM, Ashrafi K. PMID: 32675325.
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Spectroscopic coherent Raman imaging of Caenorhabditis elegans reveals lipid particle diversity. Nat Chem Biol. 2020 10; 16(10):1087-1095. Chen WW, Lemieux GA, Camp CH, Chang TC, Ashrafi K, Cicerone MT. PMID: 32572275.
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Intestinal peroxisomal fatty acid Ã-oxidation regulates neural serotonin signaling through a feedback mechanism. PLoS Biol. 2019 12; 17(12):e3000242. Bouagnon AD, Lin L, Srivastava S, Liu CC, Panda O, Schroeder FC, Srinivasan S, Ashrafi K. PMID: 31805041.
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Age- and stress-associated C. elegans granulins impair lysosomal function and induce a compensatory HLH-30/TFEB transcriptional response. PLoS Genet. 2019 08; 15(8):e1008295. Butler VJ, Gao F, Corrales CI, Cortopassi WA, Caballero B, Vohra M, Ashrafi K, Cuervo AM, Jacobson MP, Coppola G, Kao AW. PMID: 31398187.
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Tau/MAPT disease-associated variant A152T alters tau function and toxicity via impaired retrograde axonal transport. Hum Mol Genet. 2019 05 01; 28(9):1498-1514. Butler VJ, Salazar DA, Soriano-Castell D, Alves-Ferreira M, Dennissen FJA, Vohra M, Oses-Prieto JA, Li KH, Wang AL, Jing B, Li B, Groisman A, Gutierrez E, Mooney S, Burlingame AL, Ashrafi K, Mandelkow EM, Encalada SE, Kao AW. PMID: 30590647.
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The mTOR Target S6 Kinase Arrests Development in Caenorhabditis elegans When the Heat-Shock Transcription Factor Is Impaired. Genetics. 2018 11; 210(3):999-1009. Chisnell P, Parenteau TR, Tank E, Ashrafi K, Kenyon C. PMID: 30228197.
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Kynurenic acid accumulation underlies learning and memory impairment associated with aging. Genes Dev. 2018 01 01; 32(1):14-19. Vohra M, Lemieux GA, Lin L, Ashrafi K. PMID: 29386332.
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The beneficial effects of dietary restriction on learning are distinct from its effects on longevity and mediated by depletion of a neuroinhibitory metabolite. PLoS Biol. 2017 Aug; 15(8):e2002032. Vohra M, Lemieux GA, Lin L, Ashrafi K. PMID: 28763436.
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Phenotypic, chemical and functional characterization of cyclic nucleotide phosphodiesterase 4 (PDE4) as a potential anthelmintic drug target. PLoS Negl Trop Dis. 2017 Jul; 11(7):e0005680. Long T, Rojo-Arreola L, Shi D, El-Sakkary N, Jarnagin K, Rock F, Meewan M, Rascón AA, Lin L, Cunningham KA, Lemieux GA, Podust L, Abagyan R, Ashrafi K, McKerrow JH, Caffrey CR. PMID: 28704396.
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Investigating Connections between Metabolism, Longevity, and Behavior in Caenorhabditis elegans. Trends Endocrinol Metab. 2016 08; 27(8):586-596. Lemieux GA, Ashrafi K. PMID: 27289335.
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Conserved Genetic Interactions between Ciliopathy Complexes Cooperatively Support Ciliogenesis and Ciliary Signaling. PLoS Genet. 2015 Nov; 11(11):e1005627. Yee LE, Garcia-Gonzalo FR, Bowie RV, Li C, Kennedy JK, Ashrafi K, Blacque OE, Leroux MR, Reiter JF. PMID: 26540106.
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Neural Regulatory Pathways of Feeding and Fat in Caenorhabditis elegans. Annu Rev Genet. 2015; 49:413-38. Lemieux GA, Ashrafi K. PMID: 26473379.
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Stressing about misplaced fat is a key to longevity. Elife. 2015 Aug 19; 4. Lemieux GA, Ashrafi K. PMID: 26287524.
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Kynurenic acid is a nutritional cue that enables behavioral plasticity. Cell. 2015 Jan 15; 160(1-2):119-31. Lemieux GA, Cunningham KA, Lin L, Mayer F, Werb Z, Ashrafi K. PMID: 25594177.
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Insights and challenges in using C. elegans for investigation of fat metabolism. Crit Rev Biochem Mol Biol. 2015 Jan-Feb; 50(1):69-84. Lemieux GA, Ashrafi K. PMID: 25228063.
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OCT1 is a high-capacity thiamine transporter that regulates hepatic steatosis and is a target of metformin. Proc Natl Acad Sci U S A. 2014 Jul 08; 111(27):9983-8. Chen L, Shu Y, Liang X, Chen EC, Yee SW, Zur AA, Li S, Xu L, Keshari KR, Lin MJ, Chien HC, Zhang Y, Morrissey KM, Liu J, Ostrem J, Younger NS, Kurhanewicz J, Shokat KM, Ashrafi K, Giacomini KM. PMID: 24961373.
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Loss of a neural AMP-activated kinase mimics the effects of elevated serotonin on fat, movement, and hormonal secretions. PLoS Genet. 2014 Jun; 10(6):e1004394. Cunningham KA, Bouagnon AD, Barros AG, Lin L, Malard L, Romano-Silva MA, Ashrafi K. PMID: 24921650.
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Defects in the C. elegans acyl-CoA synthase, acs-3, and nuclear hormone receptor, nhr-25, cause sensitivity to distinct, but overlapping stresses. PLoS One. 2014; 9(3):e92552. Ward JD, Mullaney B, Schiller BJ, He LD, Petnic SE, Couillault C, Pujol N, Bernal TU, Van Gilst MR, Ashrafi K, Ewbank JJ, Yamamoto KR. PMID: 24651852.
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Dopamine signaling regulates fat content through Ã-oxidation in Caenorhabditis elegans. PLoS One. 2014; 9(1):e85874. Barros AG, Bridi JC, de Souza BR, de Castro Júnior C, de Lima Torres KC, Malard L, Jorio A, de Miranda DM, Ashrafi K, Romano-Silva MA. PMID: 24465759.
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Sumoylated NHR-25/NR5A regulates cell fate during C. elegans vulval development. PLoS Genet. 2013; 9(12):e1003992. Ward JD, Bojanala N, Bernal T, Ashrafi K, Asahina M, Yamamoto KR. PMID: 24348269.
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In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding. PLoS Biol. 2013 Nov; 11(11):e1001712. Lemieux GA, Keiser MJ, Sassano MF, Laggner C, Mayer F, Bainton RJ, Werb Z, Roth BL, Shoichet BK, Ashrafi K. PMID: 24260022.
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Effects of Caenorhabditis elegans sgk-1 mutations on lifespan, stress resistance, and DAF-16/FoxO regulation. Aging Cell. 2013 Oct; 12(5):932-40. Chen AT, Guo C, Dumas KJ, Ashrafi K, Hu PJ. PMID: 23786484.
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AMP-activated kinase links serotonergic signaling to glutamate release for regulation of feeding behavior in C. elegans. Cell Metab. 2012 Jul 03; 16(1):113-21. Cunningham KA, Hua Z, Srinivasan S, Liu J, Lee BH, Edwards RH, Ashrafi K. PMID: 22768843.
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Analyses of C. elegans fat metabolic pathways. Methods Cell Biol. 2012; 107:383-407. Barros AG, Liu J, Lemieux GA, Mullaney BC, Ashrafi K. PMID: 22226531.
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Hyperactive neuroendocrine secretion causes size, feeding, and metabolic defects of C. elegans Bardet-Biedl syndrome mutants. PLoS Biol. 2011 Dec; 9(12):e1001219. Lee BH, Liu J, Wong D, Srinivasan S, Ashrafi K. PMID: 22180729.
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A whole-organism screen identifies new regulators of fat storage. Nat Chem Biol. 2011 Apr; 7(4):206-13. Lemieux GA, Liu J, Mayer N, Bainton RJ, Ashrafi K, Werb Z. PMID: 21390037.
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A stress-responsive system for mitochondrial protein degradation. Mol Cell. 2010 Nov 12; 40(3):465-80. Heo JM, Livnat-Levanon N, Taylor EB, Jones KT, Dephoure N, Ring J, Xie J, Brodsky JL, Madeo F, Gygi SP, Ashrafi K, Glickman MH, Rutter J. PMID: 21070972.
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Regulation of C. elegans fat uptake and storage by acyl-CoA synthase-3 is dependent on NR5A family nuclear hormone receptor nhr-25. Cell Metab. 2010 Oct 06; 12(4):398-410. Mullaney BC, Blind RD, Lemieux GA, Perez CL, Elle IC, Faergeman NJ, Van Gilst MR, Ingraham HA, Ashrafi K. PMID: 20889131.
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mTOR complex-2 activates ENaC by phosphorylating SGK1. J Am Soc Nephrol. 2010 May; 21(5):811-8. Lu M, Wang J, Jones KT, Ives HE, Feldman ME, Yao LJ, Shokat KM, Ashrafi K, Pearce D. PMID: 20338997.
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Caenorhabditis elegans as an emerging model for studying the basic biology of obesity. Dis Model Mech. 2009 May-Jun; 2(5-6):224-9. Jones KT, Ashrafi K. PMID: 19407330.
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Rictor/TORC2 regulates Caenorhabditis elegans fat storage, body size, and development through sgk-1. PLoS Biol. 2009 Mar 03; 7(3):e60. Jones KT, Greer ER, Pearce D, Ashrafi K. PMID: 19260765.
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Fat rationing in dauer times. Cell Metab. 2009 Feb; 9(2):113-4. Cunningham KA, Ashrafi K. PMID: 19187769.
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C. elegans fat storage and metabolic regulation. Biochim Biophys Acta. 2009 Jun; 1791(6):474-8. Mullaney BC, Ashrafi K. PMID: 19168149.
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A TRPV channel modulates C. elegans neurosecretion, larval starvation survival, and adult lifespan. PLoS Genet. 2008 Oct; 4(10):e1000213. Lee BH, Ashrafi K. PMID: 18846209.
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Neural and molecular dissection of a C. elegans sensory circuit that regulates fat and feeding. Cell Metab. 2008 Aug; 8(2):118-31. Greer ER, Pérez CL, Van Gilst MR, Lee BH, Ashrafi K. PMID: 18680713.
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Serotonin regulates C. elegans fat and feeding through independent molecular mechanisms. Cell Metab. 2008 Jun; 7(6):533-44. Srinivasan S, Sadegh L, Elle IC, Christensen AG, Faergeman NJ, Ashrafi K. PMID: 18522834.
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Impaired processing of FLP and NLP peptides in carboxypeptidase E (EGL-21)-deficient Caenorhabditis elegans as analyzed by mass spectrometry. J Neurochem. 2007 Jul; 102(1):246-60. Husson SJ, Janssen T, Baggerman G, Bogert B, Kahn-Kirby AH, Ashrafi K, Schoofs L. PMID: 17564681.
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Obesity and the regulation of fat metabolism. WormBook. 2007 Mar 09; 1-20. Ashrafi K. PMID: 18050496.
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Mapping out starvation responses. Cell Metab. 2006 Apr; 3(4):235-6. Ashrafi K. PMID: 16581000.
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Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature. 2003 Jan 16; 421(6920):268-72. Ashrafi K, Chang FY, Watts JL, Fraser AG, Kamath RS, Ahringer J, Ruvkun G. PMID: 12529643.
Kaveh Ashrafi earned his undergraduate degree in Biochemistry from Virginia Tech before pursuing a PhD in Molecular Cell Biology and Biochemistry at Washington University School of Medicine. He completed subsequent postdoctoral research at Harvard Medical School and The Massachusetts General Hospital before joining the UCSF department of Physiology as Assistant Professor.
Dr. Ashrafi holds a number of awards including a Jack D. and DeLoris Lange Endowed Chair in Systems Physiology, two Haile T. Debas Academy of Educators Excellence in Teaching Awards from UCSF, and a Kaiser Award for Excellence in Teaching. In addition to being an Associate Professor for the Department of Physiology, he is faculty in the PIBS Graduate Program as well as the BMS Graduate Program and affiliated with the Cardiovascular Research Institute.
Patricial Caballero, Laboratory Assistant
George Lemieux, Associate Specialist
Mihir Vohra, Graduate Student (Neuroscience)
Lin Lin, Postdoctoral Fellow
Peter Chisnell, Graduate Student (Neuroscience)
Aude Bouagnon, Graduate Student (Biomedical Sciences)
Masako Asahina, Research Associate
Nina Riehs, Postdoc
Cecile Florence Louise M Jacovetti, Postdoc