NUTRITIONAL REGULATION OF AGING AND DISEASE

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1004235
• Project Start Date: Oct 1, 2014
• Project End Date: Sep 30, 2019
• Program Code: [(N/A)]- (N/A)

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

Performing Department
Nutritional Sciences

Non Technical Summary
The quality and quantity of food significantly impact our health and lifespan. It is known for over 80 years that low calorie diet, or dietary restriction (DR), increases lifespan for up to 50% in mammals. DR induces profound physiological changes associated with healthier life, such as decreased levels of blood glucose, insulin, triglyceride, cholesterol, and increased glucose tolerance and insulin sensitivity. In addition, this dietary regimen also prevents seemingly unrelated diseases of aging, including cancer, tissue degeneration, metabolic syndrome and immune dysfunction. 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 physiological changes at the molecular level and search for pharmaceutical interventions to mimic DR response. 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 burden to our society.

Animal Health Component

(N/A)

Research Effort Categories

Basic

100%

Applied

(N/A)

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
702	3840	1010	100%

Knowledge Area
702 - Requirements and Function of Nutrients and Other Food Components;

Subject Of Investigation
3840 - Laboratory animals;

Field Of Science
1010 - Nutrition and metabolism;

Keywords

dietary restriction

aging

circadian

Goals / Objectives
Aging is a degenerative process resulting in increased susceptibility to a wide spectrum of diseases and progressive physiological decline. A large number of physiological events follow circadian rhythms, including eating, sleeping, hormone and neurotransmitter secretion, and proficiency at cognitive tasks. Circadian disruption can result in disorders, such as obesity, diabetes, and brain dysfunction. These observations lead us to hypothesize that disruption of circadian clock might contribute to aging-associated degeneration and diseases. We propose to address fundamental questions related to the circadian control of metabolism, aging, and disease. How is the circadian clock disrupted with aging? Does circadian disruption contribute to aging-associated metabolic perturbation and physiological decline? Does nutritional stress impinge upon the circadian clock to influence the aging process? Is aging-associated circadian disruption reversible? We will employ multidisciplinary approaches, including mouse genetics, genomics, metabolomics, and biochemistry.

Project Methods
Aim 1. Determine the effects of aging and nutritional stress on the reprogramming of the clock.Recent work has provided exciting insight into reprogramming of the circadian clock by nutritional challenge [1]. Using high-throughput profiling of the liver metabolome and transcriptome, Dr. Sassone-Corsi and colleagues found that a high fat diet causes a profound reorganization of specific metabolic pathways, leading to widespread remodeling of the circadian clock in the liver. This reorganization includes a phase advance of metabolite and transcript oscillations, an abolition of otherwise oscillating transcripts and metabolites, and a surprisingly elaborate induction of newly oscillating transcripts and metabolites. We will apply an established high-throughput profiling approach combining metabolome and transcriptome to dissect the effects of aging and calorie restriction on reorganization of metabolic pathways and remodeling of the circadian clock. We will focus on two tissues. One is the liver, where a large number of metabolites are circadian controlled [2]. Another one is the suprachiasmatic nucleus (SCN) of the anterior hypothalamus, which responds to the light-dark cycles and coordinates rhythms of various aspects of circadian control [3].The calorie restriction mouse model is well established in my laboratory [4-6]. Briefly, single-caged wild type C57BL/6 mice will be fed daily with 30% reduction in calorie intake for 3 months. We will collect tissues from calorie restricted mice and control mice fed ad libitum, young mice (3 month old) and old mice (2 year old) every 4 hours throughout the circadian cycle. We will perform high throughput profiling of the metabolome and transcriptome. Metabolomic profiles will be obtained by tandem mass spectrometry (MS/MS) and gas chromatography-mass spectrometry (GC-MS). Microarrays will be performed for transcriptome profiling. Gene annotation will be performed using Genecodis. We will determine the effects of calorie restriction and aging on the phase and amplitude of oscillatory metabolites and transcripts. We will also determine the coherence of the metabolome and the transcriptome by integrating the data using the bioinformatics resource, CircadiOmics. For statistical analysis of rhythmic metabolites and transcripts, the nonparametric test JTK_CYCLE will be used, incorporating a window of 20-28 hours for the determination of circadian periodicity.Aim 2. Determine the effects of aging and nutritional stress on the CLOCK:BMAL1 complex.At the cellular level, circadian rhythms are controlled by transcriptional feedback loops that produce oscillations in gene expression [7-12]. Specialized factors, such as CLOCK and BMAL1, control rhythmicity in transcription. Activation by CLOCK:BMAL1 of target gene promoters has been linked to oscillations of numerous metabolites[13]. We will investigate the molecular mechanisms by which circadian oscillations are disrupted by aging and nutritional stress. Specifically, we will determine the effects of aging and nutritional stress on the cyclic transcription of the core clock genes, posttranslational modifications of BMAL1, as well as the chromatin recruitment of the CLOCK:BMAL1 complex.Recent studies show that a high fat diet leads to the disruption of the normal circadian cycle in part due to impaired chromatin recruitment of the CLOCK:BMAL1 complex [1]. These observations suggest that an essential modulator(s) of the CLOCK:BMAL1 complex is subject to nutritional regulation. Identification of the nutrient sensing modulator(s) associated with the CLOCK:BMAL1 complex is of paramount importance, because the effects of the diet on the clock are reversible [1], giving hope for novel therapeutic strategies.SIRT7 was recently discovered to be a chromatin-binding protein [22]. Recent studies from my laboratory show that SIRT7 deficient mice have perturbed metabolic homeostasis, prominently perturbed lipid metabolism and the development of fatty livers [23]. These observations suggest that SIRT7 functions at chromatin to regulate lipid metabolic homeostasis. Importantly, we also found that the expression of SIRT7 is suppressed by high fat feeding or aging, suggesting that this regulatory program is perturbed by overnutrition or aging. Moreover, our preliminary studies show that the circadian clock in the livers of SIRT7 deficient mice was perturbed. These observations raise the intriguing possibility that SIRT7 may function as a nutrient sensing modulator of the CLOCK:BMAL1 complex.To test this possibility, we will take a biochemical approach and determine whether SIRT7 physically interacts with the CLOCK:BMAL1 complex and co-occupies the promoter regions of their downstream targets. We will also determine whether SIRT7 is essential for the recruitment of the CLOCK:BMAL1 complex to the chromatin. We will further take a mouse genetic approach and determine whether SIRT7 deficiency results in perturbed circadian clock and reorganized metabolic pathways, mirroring the effects of a high fat diet or aging. Livers and the SCN from wild type and SIRT7 knockout mice will be collected throughout the circadian cycle for high throughput profiling of metabolome and transcriptome. The combined biochemical and mouse genetic studies proposed above may lead to the elucidation of a dynamic molecular interplay that has important implications in the pathophysiology associated with overnutrition and aging.Aim 3: Search for novel regulators through which aging and nutritional stress reprogram the clock. Recent studies show that high fat diet feeding induces an unexpected de novo genesis of oscillating transcripts, resulting in a profound reorganization of specific metabolic pathways[1]. We anticipate that aging or calorie restriction may also induce de novo genesis of oscillating transcripts and metabolites. We will follow these leads to uncover novel regulators through which aging and nutritional stress reprogram the clock. We will take a bioinformatics approach and perform transcription factor motif analysis using MotifMap on a region located 10kb upstream and 3kb downstream of the transcription start sites of the transcripts oscillating specifically under calorie restriction or aging. We will further biochemically validate the role of these candidate regulators through which aging or calorie restriction reprogram the clock. Specifically, we will determine whether their expression levels or chromatin recruitment are affected by aging or calorie restriction.Aim 4. Determine the reversibility of aging-associated circadian disruptionThe studies proposed in Aim 2 and 3 will not only provide mechanistic insights on how aging and nutritional stress reprogram the clock, but also suggest molecular approaches that can be used to potentially reverse aging-associated circadian disruption. If the studies proposed in Aim 2 indicate that SIRT7 indeed regulates chromatin recruitment of the CLOCK:BMAL1 complex and SIRT7 repression contributes to aging or high fat diet-induced abolition of oscillating transcripts and metabolites, we will determine whether reintroduction of SIRT7 reverts the effects of aging and high fat diet on the clock. We will reintroduce SIRT7 back to the livers of aged or high fat diet fed mice via AAV8-mediated gene transfer.Similarly, if studies proposed in Aim 3 lead to the identification of novel regulators through which aging or calorie restriction induces de novo genesis of oscillating transcripts and metabolites, we will determine whether inhibiting aging-induced regulators or overexpressing calorie restriction-induced regulators through AAV8-mediated gene transfer reverses aging-associated circadian disruption.

Progress 10/01/14 to 09/30/19

Outputs
Target Audience:In this reporting peroid, we have conducted experiments to determine the molecular mechanisms of stem cell aging and metabolic deregulation. I have presented our reserach at: American Society of Human Genetics, San Diego, CA Gerontological Society of America (GSA), Boston, MA Shanghai Jiaoton University Women in Science Workshop, Shanghai 4/7 Genome Dynamics in Neuroscience 7, Herzliya, Isreal University of Rochester, Rochester, NY NIH workshop for the Hematopoietic Response to Stress, Washington DC University of California, San Francisco, CA American Aging Association, San Francisco FASEB Regulation of Glucose Metabolism, Rancho Mirage, CA FASEB NAD Metabolism and Signaling, Dublin, Ireland American Society of Animal Science Meeting, Austin, TX Aging and Drug Discovery Conference, Basel, Switzerland Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Rika Ohkubo (GS) Andrew Widjaja (GS) Wei-Chieh Mu (GS) Yeong RIm Lee (GS) Zehan Song (GS) Mingdian Tan (PD) Chih-Ling Wang (PD) Jennifer Huang (UGS) Dorothy Li (UGS) Saumya Bharti (UGS) Irene Yum (UGS) Carolyn Wei (UGS) How have the results been disseminated to communities of interest?We have presented the results in national and international conferences. We have published two papers. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? In this report period, we have gained knowledge in hematopoietic stem cell aging. We have investigated how mitochondrial stress leads to HSC aging.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Mitochondrial Stress-Initiated Aberrant Activation of the NLRP3 Inflammasome Regulates the Functional Deterioration of Hematopoietic Stem Cell Aging. Luo H, Mu WC, Karki R, Chiang HH, Mohrin M, Shin JJ, Ohkubo R, Ito K, Kanneganti TD, Chen D. Cell Rep. 2019 Jan 22;26(4):945-954.e4. doi: 10.1016/j.celrep.2018.12.101.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: The Epigenetics of Stem Cell Aging Comes of Age. Chen D, Kerr C. Trends Cell Biol. 2019 Jul;29(7):563-568. doi: 10.1016/j.tcb.2019.03.006. Epub 2019 Apr 25. Review.

Progress 10/01/17 to 09/30/18

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 6 UC Berkeley graduate students, 1 postdoc, and 8 UC Berkeley undergraduate students. I have presented our research at: 10/5 FASEB Leukocyte Biology Society, Vancouver, Canada 11/9 Alliance for Healthy Aging Conference, Groningen, the Netherlands 11/30 Pennington Biomedical Research Center, Baton Rouge, LA 12/11 University of Miyazaki, Japan 2018 2/18 Keystone Innate Immunity in Disease, Vancouver, British Columbia, Canada 5/2 Stanford Diabetes Research Center Symposium, Stanford, CA 5/4 American Association of Immunology, Austin, TX 5/21 NIA The Epigenetic Regulation of Stem Cell Aging workshop, Washington DC 5/23 National Advisory Council on Aging, Washington DC 6/4 SFRR International, Lisbon, Portugal 6/22 American Diabetes Association 78th Scientific Session, Orlando, FL 6/27 NIA, Baltimore, MD 8/28 St. Jude Children's Research Hospital, Memphis, TN Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Dorothy Li (UGS) How have the results been disseminated to communities of interest? We have presented the results in national and international conferences. We have published two papers. What do you plan to do during the next reporting period to accomplish the goals? We will continue to identify novel regulators and mechanisms of hematopoietic stem cell aging.

Impacts
What was accomplished under these goals? In this reporting period, we have gained knowledge in hematopoietic stem cell aging. We have performed several experiments to determine when mitochondrial unfolded protein response is activated in hematopoietic stem cells. We have also investigated how mitochondrial stress leads to HSC aging.

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Mohrin, M.*, Widjaja, A.*, Liu, Y., Luo, H., and Chen, D. (2018) The Mitochondrial Unfolded Protein Response is Activated upon Hematopoietic Stem Cell Exit from Quiescence. Aging Cell. 17(3):e12756

Progress 10/01/16 to 09/30/17

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 7 UC Berkeley graduate students and 7 UC Berkeley undergraduate students. I have presented our research at: 10/1 2nd International Conference on Aging and Disease, Stanford, CA 11/30 Baylor University, TX 12/3 ASH, San Diego, CA 12/7 University of Kansas Medical School, Kansas City, KS 2017 1/14 Keystone Mitochondria symposia, Taos, New Mexico 4/24 Symposia at Experimental Biology, Chicago 5/1 Cincinnati Children's Hospital, OH 5/2 Women in Bio event, Panel discussion on aging research, Calico, San Francisco, CA 7/9 FASEB NAD meeting, New Orleans 8/6 FASEB HDAC meeting, Big Sky, Montana 9/27 NCI lead NIHD wide workshop: Circadian Rhythm and chronomedicine for cancer and other diseases in the era of precision medicine Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training or professional development: Hanzhi Luo (GS) Hou-Hsieh Chiang (GS) Zhifang Zhang (GS) Panayota Rigas (GS) Rika Ohkubo (GS) Andrew Widjaja (GS) Wei-Chieh Mu (GS) Albert Susanto (UGS) Daniella Melamed (UGS) Kathleen Dea (UGS) Albert Ying (UGS) Jennifer Huang (UGS) Allen Chen (UGS) Kathryn Alayvilla (UGS) How have the results been disseminated to communities of interest?We are working on a manuscript to publish the research finding. We have presented the results in national and international conferences. What do you plan to do during the next reporting period to accomplish the goals?We will continue to identify novel regulators and mechanisms of hematopoietic stem cell aging.

Impacts
What was accomplished under these goals? In this reporting period, we have gained knowledge in hematopoietic stem cell aging. We have performed several experiments to determine when mitochondrial unfolded protein response is activated in hematopoietic stem cells.

Publications

• Type: Journal Articles Status: Published Year Published: 2017 Citation: Luo, H., Chiang, H., Louw, M., Susanto, A, and Chen, D. (2017) Nutrient Sensing and the Oxidative Stress Response. Trends in Endocrinology & Metabolism. 28(6):449-460
• Type: Journal Articles Status: Published Year Published: 2017 Citation: 1. Ohkubo, R. and Chen, D. (2017) Aging: rewiring the circadian clock. Nature Structural & Molecular Biology. 24(9): 687-8.

Progress 10/01/15 to 09/30/16

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 7 UC Berkeley graduate students and 3 UC Berkeley undergraduate students. I have presented our research at: 10/27 Kavli Salon: Unraveling Neurodegeneration II, UCSF, CA 12/8 Stem Cell Center Roundtable, Berkeley, CA 2016 2/22 QB3-Calico workshop on mitochondria, UCSF 4/12 Weill Cornell Medical College, New York, NY 5/1 Keystone Aging Meeting 5/19 NIH/NIDDK Mitochondria workshop, NIH, Bethesda, MD. 6/1 University of California, San Diego, CA 6/17 Harvard Glenn Symposium, Boston, MA 7/14 Peking University, China 7/27 National Youth Leadership Forum, Berkeley, CA 8/25 ISEH, San Diego, CA Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training or professional development Jiyung Shin (graduate student) Hanzhi Luo (graduate student) Hou-Hsieh Chiang (graduate student) Zhifang Zheng (graduate student) Panayota Rigas (graduate student) Rika Ohkubo (graduate student) Makensie Louw (graduate student) Albert Susanto (undergraduate student) Daniella Melamed (undergraduate student) Kathleen Dea (undergraduate student) How have the results been disseminated to communities of interest?We are working on a manuscript to publish the research finding. We have presented the results in national and international conferences. What do you plan to do during the next reporting period to accomplish the goals?We will continue to identify novel regulators and mechanisms of hematopoietic stem cell aging.

Impacts
What was accomplished under these goals? In this reporting period, we have gained knowledge in hematopoietic stem cell aging. We identified SIRT2, a cytosolic NAD-dependent deacetylase, asa new regulator of hematopoietic stem cell aging. SIRT2 is required for the maintenance and regenerative capacity of hematopoietic stem cells at an old but not a youngage. SIRT2 expression is reduced with age in hematopoietic stem cells and overexpression of SIRT2 improves the maintenance and regenerative capacity of aged hematopoietic stem cells.

Publications

• Type: Journal Articles Status: Published Year Published: 2015 Citation: Shin, J., Mohrin, M., and Chen, D. (2015) Reversing stem cell aging. Oncotarget. 6 (17): 14723-4.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Mohrin, M. and Chen, D. (2016) The mitochondrial metabolic checkpoint and aging of hematopoietic stem cells. Current Opinion Hematology. 23(4):318-24.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Shin, J. and Chen, D. (2016) Molecular, Cellular, and Physiological Characterization of SIRT7. Methods Mol Biol. 1436:271-7.

Progress 10/01/14 to 09/30/15

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 3 postdoctoral scientists, 1 medical fellow, 6 UC Berkeley graduate students, and 1 UC Berkeley undergraduate students. I have presented our research at: 2014 10/4 UC Berkeley's 2nd Annual Stem Cell Conference, 10/9 Montagna Symposium on the Biology of Skin, Salishan, OR. 2015 1/12 UC Irvine, CA 1/16 Buck Institute, Novato, CA 2/22 Keystone hematopoiesis meeting 3/22 Keystone fatty liver meeting 4/7 Shanghai Jiaotong University, Shanghai, China. 4/8 Shanghai Fudan University, Shanghai, China 6/24 Oxygen Club of California World Congress - Oxidants and Antioxidants in Biology. Valencia, Spain. 7/19 Cell Symposia: Multifaceted Mitochondria, Chicago, IL 8/16 FASEB meeting on HDAC, sirtuins, reversible lysine modifications. Hamburg, Germany. 9/23 The Estee Lauder Companies Inc. New York, NY 9/24 NIH workshop on aging and Lung Disease, NIH, Bethesda, MD. We have established collaborations with Cole Haynes at Sloan Kettering Cancer Center, Jacob Corn at UC Berkeley. 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) Yannan Xi (postdoctoral associate) Jenny Shin (graduate student) Hanzhi Luo (graduate student) Hou-Hsieh Chiang (graduate student) Zhifang Zheng (graduate student) Panayota Rigas (graduate student) Rika Ohkubo (graduate student) Phoebe Jen (undergraduate student) How have the results been disseminated to communities of interest?We have published the results in a high impact journal, Science. We have presented the results in national and international conferences. What do you plan to do during the next reporting period to accomplish the goals?We will continue to identify novel regulators and mechanismsof hematopoietic stem cell aging.

Impacts
What was accomplished under these goals? In this reporting period, we have gained knowledge in hematopoietic stem cell aging. We identified a regulatory branch of the mitochondrial unfolded protein response (UPRmt), which is mediated by the interplay of SIRT7 and NRF1 and is coupled to cellular energy metabolism and proliferation. SIRT7 inactivation caused reduced quiescence, increased mitochondrial protein folding stress (PFSmt), and compromised regenerative capacity of hematopoietic stem cells (HSCs). SIRT7 expression was reduced in aged HSCs, and SIRT7 up-regulation improved the regenerative capacity of aged HSCs. These findings define the deregulation of a UPRmt-mediated metabolic checkpoint as a reversible contributing factor for HSC aging. This study was published in Science.

Publications

• Type: Journal Articles Status: Published Year Published: 2015 Citation: Mohrin, M.*, Shin, J.*, Liu, Y.*, Brown, K.*, Luo, H., Xi, Y., Haynes, C., and Chen, D. (2015) A Mitochondrial UPR-mediated Metabolic Checkpoint Regulates Hematopoietic Stem Cell Aging. Science 347 (6228): 1374-77.