Molecular Mechanism of Dietary Restriction's Protection Against Aging and Diseases of Aging

MOLECULAR MECHANISM OF DIETARY RESTRICTION'S PROTECTION AGAINST AGING AND DISEASES OF AGING

Sponsoring Institution

National Institute of Food and Agriculture

Project Status

TERMINATED

Funding Source

HATCH

Reporting Frequency

Annual

Accession No.

0218571

Grant No.

(N/A)

Project No.

CA-B-NTS-0006-H

Proposal No.

(N/A)

Multistate No.

(N/A)

Program Code

(N/A)

Project Start Date

Oct 1, 2009

Project End Date

Sep 30, 2014

Grant Year

(N/A)

Project Director
Chen, D.

Recipient Organization
UNIVERSITY OF CALIFORNIA, BERKELEY
(N/A)
BERKELEY,CA 94720

Performing Department
Nutritional Sciences

Non Technical Summary
Dietary intake significantly impacts our health and lifespan. Dietary restriction (DR) results in physiological changes associated with healthier life and increases lifespan. On the other hand, high fat high calorie diet is a major environmental factor for metabolic syndrome that has reached epidemic proportions in our society. It is therefore timely to understand how DR leads to beneficial physiolgical changes at the molecular level and search for pharmaceutical interventions that give the same beneficial effects as this diet. The development of DR mimetics for intervention or even treatment of diseases of aging will greatly improve the quality of life especially in the aged population and reduce the health care burdon to our society. One major research area is to understand how DR prevents metabolic disorders by eliciting favorable metabolic changes. We aim to identify the genes that regulate the DR-induced metabolic changes. These studies may provide new avenues for therapeutic intervention in metabolic syndrome. The other major research area is to understand how DR prevents tissue function decline and tumorigenesis by modulating stem cell function. Stem cells are required for tissue maintenance throughout our whole life and derailed stem cell function results in cancer. DR reverses the compromised regenerative potential of aged stem cells and the underlied molecular mechanism is under investigation.

Animal Health Component

100%

Research Effort Categories

Basic

(N/A)

Applied

(N/A)

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
302	3840	1010	10%
302	3840	1040	20%
302	3840	1080	10%
302	3840	1160	10%
303	3840	1010	10%
303	3840	1040	20%
303	3840	1080	10%
303	3840	1160	10%

Knowledge Area
302 - Nutrient Utilization in Animals; 303 - Genetic Improvement of Animals;

Subject Of Investigation
3840 - Laboratory animals;

Field Of Science
1080 - Genetics; 1010 - Nutrition and metabolism; 1160 - Pathology; 1040 - Molecular biology;

Keywords

Goals / Objectives
Our research aims to explore the molecular mechanisms of how DR slows the progression of aging and ameliorates diseases of aging in mammals. One major research area is to understand how DR prevents metabolic disorders by eliciting favorable metabolic changes. DR induces profound metabolic changes by modulating the enzymes that regulate the rate-limiting steps of metabolic pathways at both the transcriptional and the posttranscriptional levels. Cells must have evolved to efficiently shift the activities of metabolic enzymes cooperatively in response to internal or external cues. For example, during DR, gluconeogenesis and fatty acid oxidation are greatly induced, while glycolysis and fatty acid synthesis are suppressed. Coordinating the changes in these diverse metabolic pathways is critical to ensure the switch of fuel usage from glucose to fatty acids and the maintenance of blood glucose levels when food is limiting. The changes in the activity of the metabolic enzymes involved in these processes must be coordinated through a few master transcription factors at the transcriptional level and at the posttranscriptional level by enzymes that carry out posttranscriptional modifications. We propose to identify the master transcriptional factors and enzymes for posttranscriptional modifications that mediate the DR-induced metabolic changes. These studies will provide new avenues for therapeutic intervention in metabolic syndrome. The other major research area is to understand how DR prevents tissue function decline and tumorigenesis by modulating stem cell function. Aging is a multifaceted degenerative process that eventually leads to tissue function decline and increased susceptibility to diseases, such as cancer. These observations suggest that stem cells are likely to play a pivotal role in aging, because tissue maintenance throughout adult life depends on the persistence of stem cells and many cancers are believed to arise from transformed stem cells. The ability of stem cells to self-renew and repair damaged tissues decreases with age, which may account for much of the aging-associated degeneration in mammals. Our studies, as well as many others, have clearly demonstrated that while with age, stem cells have less regenerative potential and are more prone to cancer, DR is likely to keep stem cells in self-renewal, quiescent and cancer-free states. The molecular mechanisms underlying these biological processes will be studied by a systemic genome-wide screen, cell culture studies, and mouse genetics. These studies will allow us to integrate the positive and negative signals that modulate stem cell aging and regenerative potential of aged tissues. Expected outputs: During this grant period, graduate students and postdoctoral scientists will be mentored to conduct and analyzing experiments. Results will be presented at conferences and published in peer-reviewed journals.

Project Methods
More than 2000 genes, many of which encode for enzymes involved in metabolic control, are differentially regulated by DR at the transcriptional level in metabolic tissues such as the liver and the muscle. We will carry out a systemic promoter analysis for these genes, searching for transcription factors that have broad impacts on diverse metabolic pathways. We will further explore how these transcription factors are regulated by DR and what downstream events are induced through these transcription factors. The combination of genomic and biochemical approaches will be very powerful in tackling these problems. Compared to transcriptional regulation of metabolic pathways, posttranscriptional modifications of metabolic enzymes allow for a much more efficient metabolic switch. It has been postulated that acetylation of mitochondrial metabolic enzymes is likely to play a pivotal role in metabolic control. We will take a proteomic approach to examine how DR regulates these metabolic enzymes through acetylation by comparing the acetylated mitochondrial proteins in metabolic tissues from DR mice and mice fed ad libitum. We will further identify the acyltransferase(s)/deacetylase(s) that carry out the modifications of these metabolic enzymes. We hypothesize that SIRT3, a protein deaceytylase localized in mitochondria, is upregulated during DR to modulate the activities of mitochondrial enzymes and induce favorable metabolic changes. To test this hypothesis, we will take a proteomic approach to identify mitochondrial proteins regulated by SIRT3. In addition, the biological functions of SIRT3 will be explored in SIRT3 KO mice. These studies will delineate the molecular mechanisms underlying the complex metabolic regulation by CR. We will take both a candidate approach and a systemic approach to identify regulators of stem cell aging. SIRT3 is a good candidate for a regulator of hematopoietic stem cell (HSC) aging. The role of SIRT3 in HSC aging will be evaluated in SIRT3 knockout mice for phenotype related to HSC self-renewal and differentiation in young and old mice. A systemic genome-wide cDNA microarray analysis will be carried out to compare gene expression profiles of HSCs from DR mice and mice fed ad libitum. Gene ontology analysis will be carried out to uncover the biological pathways that are up- or downregulated in stem cells by DR. The effects of genes of interests on HSC function will by examined using a bone marrow transplantation assay with HSCs ectopically expressing genes of interest.

Progress 10/01/09 to 09/30/14

Outputs
Target Audience: In this reporting period, we have conducted experiments to determine the molecular mechanisms of stem cell aging and metabolic deregulation. Through these research activities, I have mentored 8 postdoctoral scientists, 14 UC Berkeley graduate students, and 18 UC Berkeley undergraduate students. I have presented our research at: 2009 UC Berkeley Stem Cell Center Retreat, Asilomar, CA East-West Alliance Meeting, Stanford, CA Children's Hospital Oakland Research Institute, Oakland, CA Homecoming 2009 Faculty Lecture, Berkeley, CA 2010 Keystone aging meeting, Lake Tahoe, CA Searle Scholar annual meeting, Chicago, IL 8th International Society of Stem Cell Research Conference, San Francisco, CA Cold Spring Harbor Laboratory Molecular Genetics of Aging, CSHL, NY The Chancellor's Forum at Berkeley, Berkeley, CA 2011 The Estee Lauder Companies Inc, New York Siebel Stem Cell Institute workshop, Berkeley, CA Searle Scholar annual meeting, Chicago, IL 9th International Society for Stem Cell Research Conference, Toronto, Canada Ellison Medical Foundation Colloquium on the Biology of Aging, Woods Hole, MA Siebel Stem Cell Institute workshop, Stanford, CA Berkeley Stem Cell Center Roundtable, Berkeley, CA The Department of Defense Office of the Congressionally Directed Medical Research Programs Breast Cancer Research Program Era of Hope Scholar Award Programmatic Review, Herndon, VA 2012 Fudan University, Shanghai, China. Keystone Sirtuin Conference, Lake Tahoe, CA. Searle Scholar annual meeting, Chicago, IL University of California, San Francisco, CA. University of California, Berkeley, CA. German-American Kavli Frontiers of Science, Potsdam, Germany. The Genetic and Environmental Toxicology Association of Northern California 2012 Symposium. Food Safety and Health in a Global Setting: The Good, the Bad, and the Ugly. Oakland, CA. Six Annual Division of Aging Biology New Investigators Forum. Bethesda, MD. Ellison Medical Foundation Colloquium on the Biology of Aging, Woods Hole, MA Massachusetts Institute of Technology, Cambridge, MA Cold Spring Harbor Molecular Genetics of Aging, NY 2012 Annual Meeting of the Society for Free Radical Biology and Medicine, San Diego, CA. Stanford University, Stanford, CA 2013 Siebel Stem Cell Institute Meeting, Berkeley, CA UC Berkeley Stem Cell Center retreat Asilomar, CA 8th Conference of the Calorie Restriction Society, Novato, CA QB3 Consortium on Healthspan Extension Workshop, San Francisco, CA Ellison Medical Foundation Colloquium on the Biology of Aging, Woods Hole, MA SENS6 Conference, Cambridge, England. University of California, San Francisco, CA. Fudan University, Shanghai, China. QB3 Symposium "The Science of Staying younger Longer", UCSF, CA Nathan Shock Aging Center Conference on Aging, San Antonio, TX Advances in Geroscience: Impact on Healthspan and Chronic Disease, NIH, Bethesda MD. 2014 Harvard Medical School, Boston, MA. Health Extension Salon, Berkeley, CA. Siebel Stem Cell Institute Meeting, Stanford, CA University of Michigan, Ann Arbor, MI. UC Berkeley Stem Cell Center retreat Asilomar, CA ISEH meeting, Montreal, Canada Cold Spring Harbor Molecular Genetics of Aging, NY. Session chair UC Berkeley's 2nd Annual Stem Cell Conference, Montagna Symposium on the Biology of Skin, Salishan, OR. We have established collaborations with many labs nationwide, such as Katrin Chua at Stanford, Fred Alt at Harvard, Eric Verdin at the Gladstone Institute, David Scadden at Harvard. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Xiaolei Qiu(postdoctoral associate, CIRM Fellowship, Siebel Fellowship, Now Senior Scientist at Siemens Healthcare Diagnostics) Dan Zhang (postdoctoral associate,Now Scientist at ReLIA Diagnostic System) Mary Mohrin (postdoctoral associate, Siebel Fellowship, NIH training grant) Ming He (specialist): Now Associate Professor at Shanghai Jiaotong University Noushin Nabavi (postdoctoral associate, Siebel Fellowship,): Now Postdoc at UCSF Rachel Whitaker (postdoctoral associate): Now Scientist at Theranos, Inc Yannan Xi (postdoctoral associate):Now Scientist at NGM Biophamaceuticals Katharine Brown, Metabolic Biology Program (graduate student): Now Postdoc at Stanford/HHMI Yufei Liu (graduate student): Now medical student at Stanford Jenny Shin (graduate student, NSF fellowship) Hanzhi Luo (graduate student) Hou-Hsieh Chiang (graduate student, James C.Y. Soong Fellowship) Zhifang Zheng (graduate student) Panayota Rigas (graduate student) Stephanie Chiao (undergraduate student, Now Medical School, UCSF) Tim Han (undergraduate student,Now Keck Graduate Institute) Ashley Shim (undergraduate student) Sandy Troung (undergraduate student,Now Medical School, Harvard) Susan Deng (undergraduate student) Yuan Liu (undergraduate student) Pamela Mar (undergraduate student,Now Medical School, U. of Southern California) Matthew Ogbuehi (undergraduate student) Samuel Lee (undergraduate student) Kathy Zheng (undergraduate student) Adele Feng (undergraduate student,Now UCSF) Connie Lee (undergraduate student) Jessica Kuo (undergraduate student) Jennifer Kim (undergraduate student) Rachel O'Hearn (undergraduate student) Elena Zhang (undergraduate student) Alina Nguyen (undergraduate student) Chalisse Fortson (undergraduate student,NIH-Bridges to Baccalaureate Summer 2014 Research Program) How have the results been disseminated to communities of interest? The results have been published in peer reviewed journals. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? One of the most fundamental questions in biology is how we age. The past decades have witnessed a significant revision of a traditional view that aging is simply a random and passive process that is solely driven by entropy. In fact, the aging process is regulated genetically and lifespan can be extended by single gene mutations. Our research aims to understand genetic and dietary interventions that regulate the aging process and explore therapeutic targets to slow aging and reverse aging-associated degeneration. The most intriguing aspect of pharmaceutical intervention that targets the aging pathways is that, instead of targeting a specific disease, it has the potential of ameliorating a wide array of seemingly unrelated diseases associated with aging, such as cancer, tissue degeneration, metabolic syndrome, and immune dysfunction. The Chen laboratory uses cell culture and genetically engineered mice to understand the molecular mechanisms of aging and to explore therapeutic approaches to prevent and treat diseases of aging.Calorie restriction (CR), a dietary regimen that extends lifespan and ameliorates a wide spectrum of diseases, and genetic regulators of aging, such as sirtuins, are used as a handle to tackle complex problems of aging. In the past five years, I have established three lines of research. a Calorie Restriction, Oxidative Stress, and Aging One major focus is to understand how CR reduces oxidative stress, a major contributor to numerous human diseases and aging. The central hypothesis is that, instead of passively slowing metabolism, CR triggers an active defense program involving a cascade of molecular regulators to reduce oxidative stress. Supporting this hypothesis is our recent finding that CR activates SIRT3, a nutrient sensor, to reduce oxidative stress (Qiu et al. Cell Metabolism, 2010). Mechanistically, we found that SIRT3 reduces oxidative stress by deacetylating and activating SOD2, a key antioxidant in the mitochondria (Qiu et al. Cell Metabolism, 2010). This finding, together with those from other laboratorieshighlights an emerging paradigm in metabolic regulation, i.e. metabolism is profoundly regulated by acetylation of metabolic enzymes and the prevalence of nutrient-sensitive reversible acetylation of metabolic enzymes allows coordination of the directionality and the rate of the metabolic flux upon changes in nutritional status (Shin et al. Molecular Cell, 2011). Our paper was well received in the field, as many other labs demonstrated that the physiological relevance of SIRT3, e.g. prevention of hearing loss and cancer, is dependent on its function to reduce oxidative stress. Since its publication in December 2010, our paper has been cited over 300 times. UC Berkeley has filed a patent based on this study, which has been approved by the US Patent Office (Patent No. 8,460,653). b Stem Cells, Aging, and Cancer The second major focus is to use hematopoietic stem cells (HSCs) as a model to understand the molecular and cellular bases of stem cell aging. CR, which greatly prevents hematopoietic senescence, improves HSC function, and suppresses myeloid leukemia development, has been used as a platform to search for genetic regulators that modulate HSC aging and diseases of HSC origin. We found that SIRT3 is highly expressed in HSCs, where it regulates the oxidative stress response. Importantly, SIRT3 expression declines with age, and SIRT3 overexpression rescues the functional defects of aged HSCs (Brown et al. Cell Reports, 2013). This study was highlighted by Editors' Choice in Science. It was also chosen as Cell Reports Best of 2013. It received numerous media coverage, including US News and World Reports, Discovery News, ABC News, Telegraph, BioWorld, Science Daily, Gizmag, AALAtimes, Daily California, etc. Since its publication in 2013, our paper has been cited over 50 times.We recently completed another study on metabolic regulation of HSCs and uncovered a novel metabolic cell cycle checkpoint regulating stem cells. A manuscript on this study is currently under submission (Mohrin, et al. in submission). c Metabolic Diseases The third major research focus investigates how overnutrition and aging perturb metabolic homeostasis, leading to the development of obesity and increased risk of numerous human diseases, such as cardiovascular disease, hypertension, cancer, and type 2 diabetes. Nonalcoholic fatty liver disease affects one-third of adults and an increasing number of children in developed countries. Its pathogenesis is poorly understood, and therapeutic options are limited. We found that SIRT7, an NAD+-dependent H3K18Ac deacetylase, functions at chromatin to provide epigenetic blockage of ER stress and prevent the development of fatty liver disease. Highlights of Research Accomplishments: · Mechanistic understanding of the beneficial effects of calorie restriction, the most robust dietary intervention for mammalian lifespan extension and disease prevention (Qiu et al., Cell Metabolism, 2010). · Mechanistic understanding of metabolic regulation. Supported a new paradigm in metabolic regulation: metabolism is profoundly regulated by acetylation of metabolic enzymes (Qiu et al., Cell Metabolism, 2010; Shin et al., Molecular Cell, 2011). This mode of regulation has profound implications in aging and aging-related diseases (Brown et al., Cell Reports, 2013). · Mechanistic understanding of stem cell aging and tissue maintenance. Provided a basis for rejuvenating aged stem cells (Brown et al., Cell Reports, 2013). · Mechanistic understanding of fatty liver disease, a prevalent metabolic disease. Provided the basis for a potential therapeutic treatment of animals with metabolic disorders (Shin et al., Cell Reports, 2013). · Mechanistic understanding of metabolic regulation of stem cell maintenance. Uncovered a novel metabolic cell cycle checkpoint in stem cells (Mohrin et al. in submission)

Publications

Type: Journal Articles Status: Published Year Published: 2014 Citation: 1. Xi, Y. and Chen, D. (2014) Partitioning the Circadian Clock. Science. 345 (6201):1122-3.

Progress 01/01/13 to 09/30/13

Outputs
Target Audience: In this reporting period, we have conducted experiments to determine the molecular mechanisms of stem cell aging and metabolic deregulation. Through these research activities, I have mentored five postdoctoral scientists, three UC Berkeley graduate students, and three UC Berkeley undergraduate students. I have presented our research at 8th Conference of the Calorie Restriction Society, SENS6 Conference, UCSF, Fudan University, Nathan Shock Aging Center Conference on Aging, and NIH Summit on Advances in Geroscience. We have established collaborations with many labs nationwide, such as Katrin Chua at Stanford, Fred Alt at Harvard, Eric Verdin at Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Training or professional development Mary Mohrin (postdoctoral associate) Ming He (specialist) Noushin Nabavi (postdoctoral associate) Rachel Whitaker (postdoctoral associate) Yannan Xi (postdoctoral associate) Yufei Liu (graduate student) Jenny Shin (graduate student) Hanzhi Luo (graduate student) Jennifer Kim (undergraduate student) Elena Zhang (undergraduate student) Rachel O’Hearn(undergraduate student) How have the results been disseminated to communities of interest? Partner Organizations: Siebel Institute – financial support Glenn Foundation - financial support Buck Institute – financial support Hellman Family Faculty Fund-financial support National Institute of Aging- financial support American Heart Association- financial support Ellison Medical Foundation- financial support University of California Office of President- financial support Gladstone Institute – collaboration Harvard-collaboration Stanford – collaboration Collaborators and contacts Eric Verdin (Gladstone Institute) David Scadden, Fred Alt (Harvard) Katrin Chua (Stanford) What do you plan to do during the next reporting period to accomplish the goals? We will futher elucidate the molecular mechanisms underlying hematopoietic stem cell maintenance and aging. Specificially, we will determine the role of SIRT7 in this context.

Impacts
What was accomplished under these goals? In this reporting period, we have gained knowledge in metabolic regulation and the development of fatty liver disease, a prevalent metabolic disease that affects one third of adults and increasing number of children in the developed countries. We found that SIRT7, a H3K18 deacetylase, functions at chromatin to suppress ER stress and prevent the development of fatty liver disease. SIRT7 is induced upon ER stress and is stabilized at the promoters of ribosomal proteins through its interaction with the transcription factor Myc to silence gene expression and to relieve ER stress. SIRT7-deficient mice develop chronic hepatosteatosis resembling human fatty liver disease. Myc inactivation or pharmacological suppression of ER stress alleviates fatty liver caused by SIRT7 deficiency. Importantly, SIRT7 suppresses ER stress and reverts the fatty liver disease in diet-induced obese mice. Our study identifies SIRT7 as a cofactor of Myc for transcriptional repression and delineates a druggable regulatory branch of the ER stress response that prevents and reverts fatty liver disease. This study was published in Cell Reports.

Publications

Type: Journal Articles Status: Accepted Year Published: 2013 Citation: 1. Shin, J.*, He, M.*, Liu, Y.*, Paredes, S.*, Villanova, L., Brown, K., Qiu, X., Nabavi, N., Mohrin, M., Wojnoonski, K., Li, P., Cheng, H., Murphy, A., Valenzuela, D., Luo, H., Kapahi, P., Krauss, R., Mostoslavsky, R., Yancopoulos, G., Alt, F., Chua, K., and Chen, D. (2013) SIRT7 Represses Myc Activity to Suppress ER Stress and Prevent Fatty Liver Disease. Cell Reports 5(3):654-665. 2. Brown, K.*, Xie, S.*, Qiu, X., Mohrin, M., Shin, J., Liu, Y., Zhang, D., Scadden, D., Chen, D. (2013) SIRT3 reverses aging-associated degeneration. Cell Reports 3(2):319-27. See also Editors choice, Science. (2013) 339: 884. See also Cell Reports Best of 2013. 3. Tia, S.Q., Brown, K., Chen, D., Herr, A.E. (2013) Protein post-translational modification analyses using on-chip immunoprobed isoelectric focusing. Anal Chem. 85(5):2882-90.

Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: In this reporting period, we have conducted experiments to determine the molecular mechanisms of stem cell aging and metabolic deregulation. Through these research activities, I have mentored three postdoctoral scientists, four UC Berkeley graduate students, one rotation students and three UC Berkeley undergraduate students. I have presented our research at Fudan University, Keystone Sirtuin Conference, Searle Scholar meeting, UC San Francisco, UC Berkeley, German-American Kavli Frontiers of Science, the Genetic and Environmental Toxicology Association of Northern California Symposium, Six Annual Division of Aging Biology New Investigators Forum, Ellison Medical Foundation Colloquium on the Biology of Aging, Massachusetts Institute of Technology, Cold Spring Harbor Molecular Genetics of Aging, Annual Meeting of the Society for Free Radical Biology and Medicine, Stanford University, and Bay Area Aging Club Symposium. We have established collaborations with many labs nationwide, such as Katrin Chua at Stanford, Tom Rando at Stanford, Fred Alt at Harvard, Eric Verdin at the Gladstone Institute, David Scadden at Harvard. PARTICIPANTS: Individuals: Principal investigator: Danica Chen Participants: Mary Mohrin, Ph.D. Ming He, Ph.D. Noushin Nabavi, Ph.D. Katharine Brown Yufei Liu Jenny Shin Hanzhi Luo Kelly Garton Partner Organizations: Kinship Foundation (Searle Scholars Program) - financial support Siebel Institute - financial support Hellman Family Faculty Fund-financial support National Institute of Aging- financial support American Heart Association- financial support Ellison Medical Foundation- financial support University of California Office of President- financial support Gladstone Institute - collaboration Harvard-collaboration Stanford - collaboration Collaborators and contacts Eric Verdin (Gladstone Institute) David Scadden, Fred Alt (Harvard) Katrin Chua, Tom Rando (Stanford) Training or professional development Mary Mohrin (postdoctoral associate) Ming He (specialist) Noushin Nabavi (postdoctoral associate) Katharine Brown (graduate student) Yufei Liu (graduate student) Jenny Shin (graduate student) Hanzhi Luo (graduate student) Kelly Garton (graduate student) Jennifer Kim (undergraduate student) Elena Zhang (undergraduate student) Rachel O'Hearn(undergraduate student) TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
In this reporting period, we have gained knowledge in how hematopietic stem cells (HSCs) age. We found that SIRT3, a mitochondrial NAD+-dependent deacetylase that regulates the global acetylation landscape of mitochondrial proteins and triggers metabolic reprogramming toward reduced oxidative stress, is highly enriched in hematopoietic stem cells (HSCs) where it regulates a stress response. SIRT3 is dispensable for HSC maintenance and tissue homeostasis at a young age under homeostatic conditions but is essential under stress or at an old age. Importantly, SIRT3 is suppressed with aging, and SIRT3 upregulation in aged HSCs improves their regenerative capacity. Our study illuminates the plasticity of mitochondrial homeostasis controlling stem cell and tissue maintenance during the aging process and shows that aging-associated degeneration can be reversed by a sirtuin. This study was published in a high impact journal Cell Reports. We have also gained knowledge in metabolic regulation. We found that SIRT7, a H3K18 deacetylase, is required to maintain lipid metabolic homeostasis. Manuscripts based on these studies are under submission for publication.

Publications

Brown, K.*, Xie, S.*, Qiu, X., Mohrin, M., Shin, J., Liu, Y., Zhang, D., Scadden, D., Chen, D. (2013) SIRT3 reverses aging-associated degeneration. Cell Reports 3(2):319-27.
Mohrin, M., and Chen, D. (2013) Sirtuins, tissue maintenance, and tumorigenesis. Genes & Cancer.
Brown, K.*, Liu, Y.*, and Chen, D. (2012) Aging: the mitochondrial connection. Clinical & Experimental Pathology.

Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: In this reporting period, we have conducted experiments to determine the molecular mechanisms of stem cell aging. Through these research activities, I have mentored two postdoctoral scientists, three UC Berkeley graduate students, two rotation students and six UC Berkeley undergraduate students. I have presented our research at the Estee Lauder Companies Inc, Siebel Stem Cell Institute workshop, Searle Scholar meeting, the Berkeley Stem Cell Center Roundtable, the Department of Defense Office of the Congressionally Directed Medical Research Programs, Breast Cancer Research Program Era of Hope Scholar Award Programmatic Review, the UC Berkeley Stem Cell Center Retreat, Ellison Medical Foundation Colloquium on the Biology of Aging, International Society for Stem Cell Research Conference, Bay Area Aging Club Symposium, the Berkeley Homecoming Faculty lecture. We have established collaborations with many labs at UC Berkeley and the bay area, such as Eric Verdin at the Gladstone Institute, David Scadden at Harvard, Changzheng Chen at Stanford. PARTICIPANTS: Individuals: Principal investigator: Danica Chen Participants: Xiaolei Qiu, Ph.D. Dan Zhang, Ph.D. Katharine Brown Yufei Liu Jenny Shin Hanzhi Luo Aparna Krishnamoorthy Partner Organizations: Kinship Foundation (Searle Scholars Program) - financial support Siebel Institute - financial support CIRM-financial support Hellman Family Faculty Fund-financial support National Institute of Aging- financial support American Heart Association- financial support Ellison Medical Foundation- financial support University of California Office of President- financial support Gladstone Institute - collaboration Harvard-collaboration UC Daivs - collaboration Stanford - collaboration Collaborators and contacts Eric Verdin (Gladstone Institute) David Scadden (Harvard) Changzheng Chen (Stanford) Training or professional development Xiaolei Qiu (postdoctoral associate) Dan Zhang (postdoctoral associate) Katharine Brown (graduate student) Yufei Liu (graduate student) Jenny Shin (graduate student) Hanzhi Luo (graduate student) Aparna Krishnamoorthy (graduate student) Matthew Ogbuehi (undergraduate student) Samuel Lee (undergraduate student) Kathy Zheng (undergraduate student) Adele Feng (undergraduate student) Connie Lee (undergraduate student) Jessica Kuo (undergraduate student) TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
In this reporting period, we have gained knowledge in how hematopietic stem cells (HSCs) age. We found that SIRT3, a mitochondrial NAD+-dependent deacetylase that regulates the global acetylation landscape of mitochondrial proteins and triggers metabolic reprogramming toward reduced oxidative stress, is highly enriched in hematopoietic stem cells (HSCs) and is suppressed in differentiated hematopoietic cells. Deletion of the SIRT3 gene in mice has no effect on the HSC pool at a young age under homeostatic conditions, but causes compromised self-renewal and differentiation of HSCs under stress or at an old age. We further show that SIRT3 expression and activity in HSCs decrease with age. Importantly, forced expression of SIRT3 in aged HSCs improves their functional capacity. Our study illuminates the plasticity of mitochondrial homeostasis controlling stem cell maintenance and tissue homeostasis during the aging process. Manuscripts based on these studies are under submission for publication.

Publications

Shin, J., Zhang, D., and Chen, D. (2011) Reversible acetylation of metabolic enzymes celebration: SIRT2 and p300 join the party. Molecular Cell. 43(1):3-5.
Zhang, D., Liu, Y., and Chen, D. (2011) SIRT-ain relief from age-inducing stress. Aging. 3(2):158-61.
Liu, Y., Zhang, D., and Chen, D. (2011) SIRT3: Striking at the heart of aging. Aging. 3(1):1-2.
Baur JA, Chen D., Chini EN, Chua K, Cohen HY, de Cabo R, Deng C, Dimmeler S, Gius D, Guarente LP, Helfand SL, Imai S, Itoh H, Kadowaki T, Koya D, Leeuwenburgh C, McBurney M, Nabeshima Y, Neri C, Oberdoerffer P, Pestell RG, Rogina B, Sadoshima J, Sartorelli V, Serrano M, Sinclair DA, Steegborn C, Tatar M, Tissenbaum HA, Tong Q, Tsubota K, Vaquero A, Verdin E. (2010) Dietary restriction: standing up for sirtuins. Science. 329(5995):1012-3.
Qiu, X., Moran, Y., Brown, K., and Chen, D. (2010) Sirtuin regulation in calorie restriction. BBA Proteins and Proteomics. 1804(8):1576-83.

Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: In this reporting period, we have conducted experiments to determine the molecular mechanisms by which calorie restriction reduces oxidative stress, a well-accepted cause of aging. We have also conducted experiments to determine the molecular mechanisms of stem cell aging. Through these research activities, I have mentored two postdoctoral scientists, two UC Berkeley graduate students, two rotation students and four UC Berkeley undergraduate students. I have presented our research at the UC Berkeley Stem Cell Center Retreat, Keystone Aging Conference, Cold Spring Harbor Aging Conference, Searle Scholars Program meeting, Bay Area Aging Club Symposium, the Chancellor's Forum. We have established collaborations with many labs at UC Berkeley and the bay area, such as Eric Verdin at the Gladstone Institute, David Scadden at Harvard, Changzheng Chen at Stanford. PARTICIPANTS: Individuals: Principal investigator: Danica Chen Participants: Xiaolei Qiu, Ph.D. Dan Zhang, Ph.D. Katharine Brown Yufei Liu Patti Liu Jenny Shin Partner Organizations: Kinship Foundation (Searle Scholars Program) - financial support Siebel Institute - financial support CIRM-financial support Hellman Family Faculty Fund-financial support Gladstone Institute - collaboration Harvard-collaboration UC Daivs - collaboration Stanford - collaboration Collaborators and contacts Eric Verdin (Gladstone Institute) David Scadden (Harvard) Changzheng Chen (Stanford) Training or professional development Xiaolei Qiu (postdoctoral associate) Dan Zhang (postdoctoral associate) Katharine Brown (graduate student) Yufei Liu (graduate student) Patti Liu (graduate student) Jenny Shin (graduate student) Stephanie Chiao (undergraduate student) Tim Han (undergraduate student) Pam Mar (undergraduate student) Ashley Shin (undergraduate student) Sandy Truong (undergraduate student) Susan Deng (undergraduate student) TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
In this reporting period, we have gained knowledge in how calorie restriction (CR) diet reduces oxidative stress. We found that CR induces the expression of SIRT3, a deacetylase localized in the mitochondria, and CR reduces oxidative stress by inducing SIRT3. We also investigated the molecular mechanisms by which SIRT3 reduces oxidative stress. SIRT3 activates SOD2, a mitochondrial antioxidant, via deacetylation, and promotes oxidative stress resistance. Since oxidative stress is considered a major cause of aging, our studies may lead to the elucidation of how CR slows aging and extends lifespan. These studies are published in Cell Metabolism. We have also gained knowledge in how hematopietic stem cells (HSCs) age. We found that, in aged mice lacking SIRT3, HSCs are more prone to apoptosis and the number of HSCs decreases, compared to control mice, suggesting that SIRT3 promotes HSC survival and mains the HSC pool as animals age. Manuscripts based on these studies are under submission for publication.

Publications

Calorie restriction reduces oxidative stress by SIRT3-mediated SOD2 activation. Qiu X, Brown K, Hirschey MD, Verdin E, Chen D. Cell Metab. 2010 Dec 1;12(6):662-7.

Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: In this reporting period, we have conducted experiments to determine the molecular mechanisms by which calorie restriction reduces oxidative stress, a well-accepted cause of aging. We have also conducted experiments to determine the molecular mechanisms of stem cell aging. Through these research activities, I have mentored two postdoctoral scientists, two UC Berkeley graduate students, two rotation students and six UC Berkeley undergraduate students. I have presented our research at the UC Berkeley Stem Cell Center Retreat, East-West Alliance Meeting, Children's Hospital Oakland Research Institute, and Homecoming Faculty Lecture. We have established collaborations with many labs at UC Berkeley and the bay area, such as Eric Verdin at the Gladstone Institute, Changzheng Chen at Stanford, Su-Ju Lin at UC Davis, Marc Hellerstein at Berkeley. PARTICIPANTS: Individuals: Principal investigator: Danica Chen Participants: Xiaolei Qiu, Ph.D. Dan Zhang, Ph.D. Katharine Brown Yufei Liu Angela Becker Dee Grisby Partner Organizations: Kinship Foundation (Searle Scholars Program) - financial support Siebel Institute - financial support Gladstone Institute - collaboration UC Daivs - collaboration Stanford - collaboration Collaborators and contacts Eric Verdin (Gladstone Institute) Su-Ju Lin (UC Davis) Changzheng Chen (Stanford) Marc Hellerstein (Berkeley) Training or professional development Xiaolei Qiu (postdoctoral associate) Dan Zhang (postdoctoral associate) Katharine Brown (graduate student) Yufei Liu (graduate student) Angela Becker (graduate student) Dee Grisby (graduate student) Stephanie Chiao (undergraduate student) Tim Han (undergraduate student) Pam Mar (undergraduate student) Ashley Shin (undergraduate student) Sandy Truong (undergraduate student) Susan Chan (undergraduate student) TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
In this reporting period, we have gained knowledge in how calorie restriction (CR) diet reduces oxidative stress. We found that CR induces the expression of SIRT3, a deacetylase localized in the mitochondria, and CR reduces oxidative stress by inducing SIRT3. We also investigated the molecular mechanisms by which SIRT3 reduces oxidative stress. SIRT3 deacetylates and activates SOD2, a mitochondrial antioxidant. In addition, SIRT3 deacetylates and activates LCAD, the enzyme catalyzing the first step of beta-oxidation, and triggers a metabolic switch from glucose to fatty acid oxidation, a process associated with decreased production of reactive oxidative species. Since oxidative stress is considered a major cause of aging, our studies may lead to the elucidation of how CR slows aging and extends lifespan. We have also gained knowledge in how hematopietic stem cells (HSCs) age. We found that, in aged mice lacking SIRT3, HSCs are more prone to apoptosis and the number of HSCs decreases, compared to control mice, suggesting that SIRT3 promotes HSC survival and mains the HSC pool as animals age. Manuscripts based on these studies are under submission for publication.

Publications

Qiu, X., Brown, K., Moran, Y., and Chen, D. (2009) Sirtuin regulation in calorie restriction. Review. BBA Proteins and Proteomics. (In press)