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    Amy K Walker PhD

    TitleAssistant Professor
    InstitutionUniversity of Massachusetts Medical School
    DepartmentProgram in Molecular Medicine
    AddressUniversity of Massachusetts Medical School
    373 Plantation Street, Room 319
    Worcester MA 01605
    Phone508-856-3645
      Other Positions
      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentInterdisciplinary Graduate Program

        Overview 
        Narrative

        How is transcriptional regulation of lipogenesis linked to diet and environment in C. elegans and mammals

        SREBP (sterol regulatory element binding protein) transcription factors activate genes important for cholesterol metabolism, fatty acid (FA) and synthesis of phospholipids, in addition to ensuring production of additional important co-factors. We have found unexplored regulatory links between lipid metabolism and the one-carbon cycle (1CC), discovering that SREBP proteins in C. elegans and mammals control expression of 1CC genes. The 1CC provides methyl groups for PL biosynthesis and epigenetic regulation; regulation by SREBPs provides a novel layer of nutrition-dependent input to methylation-dependent processes. Alterations in 1C metabolism and SREBP function are associated with similar diseases, suggesting that co-regulation with lipid homeostasis may be a common impact point in metabolic-associated disorders such as obesity and fatty liver disease.

        Most methylation reactions require SAMe (s-adenosyl methionine). Conversion of methionine to SAMe by MAT1A/MAT2A in humans, or the SAMS proteins in C. elegans, affects cellular processes from phosphatidylcholine (PC) biosynthesis to protein or DNA modification. We have found that SREBPs regulate sams-1 and MAT1A expression in both C. elegans and human cells. In C. elegans, sams-1 decrease or loss causes lipid accumulation reminiscent of hepatic steatosis occuring in MAT1A KO mice (Lu et al. PNAS 2001), suggesting models for lipid accumulation in sams-1 animals may be relevant to hepatic steatosis in mammals. Because the 1CC is implicated in multiple fatty liver models and metabolites such as folate or choline are administered as treatments for disease, it is crucial to understand the connections between the 1CC and lipid biosynthesis.

        We are interested in how lipid homeostasis is affected by genetic or dietary changes in 1CC function and how SBP-1/SREBP affects cellular processes such as epigenetic modification by regulating the supply of methyl donors. These projects will include mechanistic studies in mammalian cell culture, in vivo studies in mouse liver as well as genetics screens for discovery in C. elegans. In our studies of SREBP regulation by SIRT1 (Walker, et al. 2010, Genes and Development) and of SREBP regulation of the 1CC (Walker, A., Jacobs, R. et al., Cell, 2011), this combination of models has allowed us to rapidly establish functional biological relationships between pathways in C. elegans, then determine relevance to mammalian physiology and precise molecular mechanisms in mouse knockout or human cell culture models. These types of experiments are important for determining mechanistic relationships between metabolic pathways and cellular function, and furthermore, will aid in our understanding about how these pathways contribute to human disorders such as metabolic syndrome.

        Amy walker  - worms

        Figure. In C. elegans, SBP-1-Dependent Lipogenesis and Gene Expression Are Increased after sams-1(RNAi)

        (A) RNAi knockdown of sams-1 revealed large refractile droplets in the intestine and body cavity by Nomarski optics.

        Amy Walker - Lipid


        Rotation Projects

        Determine links between SREBPs, SAMe levels and epigenetic regulation

        Methylation of histones or DNA affects gene expression at local as well as global levels. The major cellular methyl donor, s-adenosylmethionine (SAMe) is produced by the folate or 1-carbon (1C) cycle. 1CC function may be affected by dietary levels of folate, methionine, choline or betaine, genetic polymorphisms, or alcohol intake, linking potential for epigenetic modification in cancer progression to food intake and metabolism. Physiological limitation of 1CC function has multiple deleterious physiological effects from birth defects to the development of hepatosteatosis and has also been linked to hepatic and colon cancer. While many studies have shown that the availability of methyl donors may dramatically affect human disease, the mechanisms governing SAMe production and epigenetic modification are much less clear. We hypothesize that modulation of SBP-1 function affecting sams-1 expression will also alter methyl group levels and subsequently, histone modification, leading to changes in gene expression relevant to overall nutritional homeostasis. We will determine if modulation of SAMe levels through SBP-1 effects histone methylation at nutritionally important promoters and examine how diet quality and dietary supplementation affect SBP-1 activity by evaluating histone methylation, in addition to employing biological assays for epigenetic changes in gene expression. We will also use unbiased assays such as ChIP-Seq to identify genes whose expression levels are linked to epigenetic changes after sbp-1 RNAi, selecting those with roles in metabolism for further study. These studies will provide a basis for understanding how lipid homeostasis and other dietary influences affect SAMe production and how those are linked to increased lipid accumulation in C. elegans. Future studies will extend these models to mammalian systems to investigate how these changes predispose hepatosteatosis, a component of metabolic syndrome in humans. Figure 2



        Determine mechanisms for differential regulation of SREBP-1 and SREBP-2 by PC-based feedback

        In recent studies, we have found that inactive precursors for SREBP-1 are cleaved, accumulate in the nucleus and activate lipogenic transcription programs when membrane changes linked to low PC levels alter localization of SREBP-activating proteases (see Research Interests). We also found that SREBP-2 was resistant to this regulation (Figure 1), and note that while mouse models of PC depletion are associated with hepatic steatosis, cholesterol levels are not necessarily affected (Jacobs, et al. 2008, JBC). We will determine the mechanisms of this differential regulation which will be important for understanding how lipid or cholesterol synthesis may be inappropriately stimulated in metabolic disease.

        Figure 1 
        Figure 1: Depletion of PC biosynthesis enzymes in HepG2 human hepatoma cells causes nuclear localization of SREBP-1, but not SREBP-2. Yellow line shows cell boundary


         



        Identify cellular responses to decreased SAMe production

        Our studies in C. elegans showed that SREBP transcriptional activators could control expression 1CC genes. These studies are important because they demonstrate that levels of these critical enzymes mRNAa are not controlled as a “housekeeping function” but are instead are coordinated with other cellular processes. We have developed two models for 1CC dysfunction in C. elegans, a genetic model based on loss of function (lof) of sams-1, a SBP-1/SREBP responsive gene encoding the enzyme for producing the methyl donor SAMe and a dietary model in which C. elegans are fed bacteria unable to synthesize folate. In both of these models, transcription of lipogenic genes are highly increased and sams-1(lof) worms accumulate large lipid droplets, mimicking aspects of fatty liver disease in mammals. These models will allow use genetic screens as a tool for identifying 1) other regulatory pathways affecting SAMe production or utilization and 2) cellular responses that limit lipogenesis when methyl donor levels are low.



        Bibliographic 
        selected publications
        List All   |   Timeline
        1. Amy K Walker & Anders M Näär. Clinical Lipidology. SREBPs: regulators of cholesterol/lipids as therapeutic targets in metabolic disorders, cancers and viral diseases. 2012; 1(7):27-36.
        2. Walker AK, Jacobs RL, Watts JL, Rottiers V, Jiang K, Finnegan DM, Shioda T, Hansen M, Yang F, Niebergall LJ, Vance DE, Tzoneva M, Hart AC, Näär AM. A conserved SREBP-1/phosphatidylcholine feedback circuit regulates lipogenesis in metazoans. Cell. 2011 Nov 11; 147(4):840-52.
          View in: PubMed
        3. Walker AK, Yang F, Jiang K, Ji JY, Watts JL, Purushotham A, Boss O, Hirsch ML, Ribich S, Smith JJ, Israelian K, Westphal CH, Rodgers JT, Shioda T, Elson SL, Mulligan P, Najafi-Shoushtari H, Black JC, Thakur JK, Kadyk LC, Whetstine JR, Mostoslavsky R, Puigserver P, Li X, Dyson NJ, Hart AC, Näär AM. Conserved role of SIRT1 orthologs in fasting-dependent inhibition of the lipid/cholesterol regulator SREBP. Genes Dev. 2010 Jul 1; 24(13):1403-17.
          View in: PubMed
        4. Blackwell TK, Walker AK. OMA-gosh, where's that TAF? Cell. 2008 Oct 3; 135(1):18-20.
          View in: PubMed
        5. Walker AK, Boag PR, Blackwell TK. Transcription reactivation steps stimulated by oocyte maturation in C. elegans. Dev Biol. 2007 Apr 1; 304(1):382-93.
          View in: PubMed
        6. Blackwell TK, Walker AK. Transcription mechanisms. WormBook. 2006; 1-16.
          View in: PubMed
        7. Yang F, Vought BW, Satterlee JS, Walker AK, Jim Sun ZY, Watts JL, DeBeaumont R, Saito RM, Hyberts SG, Yang S, Macol C, Iyer L, Tjian R, van den Heuvel S, Hart AC, Wagner G, Näär AM. An ARC/Mediator subunit required for SREBP control of cholesterol and lipid homeostasis. Nature. 2006 Aug 10; 442(7103):700-4.
          View in: PubMed
        8. Walker AK, Shi Y, Blackwell TK. An extensive requirement for transcription factor IID-specific TAF-1 in Caenorhabditis elegans embryonic transcription. J Biol Chem. 2004 Apr 9; 279(15):15339-47.
          View in: PubMed
        9. Blackwell TK, Walker AK. Transcription elongation: TLKing to chromatin? Curr Biol. 2003 Dec 2; 13(23):R915-6.
          View in: PubMed
        10. Takagi T, Walker AK, Sawa C, Diehn F, Takase Y, Blackwell TK, Buratowski S. The Caenorhabditis elegans mRNA 5'-capping enzyme. In vitro and in vivo characterization. J Biol Chem. 2003 Apr 18; 278(16):14174-84.
          View in: PubMed
        11. Walker AK, Blackwell TK. A broad but restricted requirement for TAF-5 (human TAFII100) for embryonic transcription in Caenorhabditis elegans. J Biol Chem. 2003 Feb 21; 278(8):6181-6.
          View in: PubMed
        12. Shim EY, Walker AK, Shi Y, Blackwell TK. CDK-9/cyclin T (P-TEFb) is required in two postinitiation pathways for transcription in the C. elegans embryo. Genes Dev. 2002 Aug 15; 16(16):2135-46.
          View in: PubMed
        13. Shim EY, Walker AK, Blackwell TK. Broad requirement for the mediator subunit RGR-1 for transcription in the Caenorhabditis elegans embryo. J Biol Chem. 2002 Aug 23; 277(34):30413-6.
          View in: PubMed
        14. Blackwell TK, Walker AK. Getting the right dose of repression. Genes Dev. 2002 Apr 1; 16(7):769-72.
          View in: PubMed
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