Modeling of Human Aging using a Systems Approach

1. Modeling of Human Aging using a Systems Approach Dissertation proposal for Glenn Booker June 5, 2008

2. Presentation Outline • Overview • Aging Theories • Gene Expression Data • Fuzzy Modeling Approach • Vicious Cycle Model • Retrograde Response Model • Network Theory of Aging • Demographic Implications • Summary Dissertation Proposal

3. Overview • My dissertation research will investigate whether changes observed at the cellular level support the existence of a retrograde response defense mechanism in human aging and whether these changes show on higher levels such as in gene-disease networks and in biodemographics Dissertation Proposal

4. Overview • There are three main elements of this research • Cellular system modeling using fuzzy logic • Investigation of network connections among changes in gene expression with age, and increased occurrence of certain diseases • Biodemographic analysis to investigate the plateau effect and its possible connection to the retrograde response Dissertation Proposal

5. Overview • The retrograde response (RR) is when a cell slows using oxidative phosphorylation (oxphos) to produce energy (ATP), and instead uses the anaerobic and much less efficient glycolysis to produce ATP • The RR has been observed in yeast and other organisms, but not in humans or other mammals (Butow, 2004) Dissertation Proposal

6. Overview • This research is described as a ‘systems approach’ because it integrates cellular level gene expression data with larger scale biological pathways, organism-level diseases and population-scale demographic data • This multiscale perspective is analogous to efforts such as the Physiome project (Hunter, 2005) Dissertation Proposal

7. Aging Theories • Dozens of theories and models have been proposed to explain why organisms age (Kirkwood, 2003; Kirkwood, 2005) • Rate of living theory (1908) – long-lived animals exert less energy per unit mass • Caloric restriction (1935) – Eating less helps you live longer • Like Mechanistic theories (1963), which say specific metabolic pathways cause aging Dissertation Proposal

8. Aging Theories • Free radical theories (1956) - Free radicals and reactive oxidative species (ROS) damage cell components (deMagalhaes, 2006; Fleury, 2002) • Shortening of telomeres theory is related to this • DNA damage (1959) – damage accumulates to DNA until the body can’t repair itself • Basis for the Vicious Cycle (VC) model • Programmed Senescence (1961) – the body is programmed to kill itself off Dissertation Proposal

9. Aging Theories • Disposable Soma Theory (1977) –focus resources on reproduction, at the expense of shorter life • A similar concept is Pleiotropy; genes which help early in life, later cause damage • Network theory of aging (1992) – which combines models of mitochondrial ROS production, aberrant proteins, free radicals, and scavengers (MARS) (Kowald, 1996) Dissertation Proposal

10. Gene Expression Data • The lab of Dr. Kriete has conducted genome-wide gene expression studies from human fibroblasts in a cross-sectional study of varying age subjects (age 17 to 94), and identified genes which are significantly (>2.5 or <1/2.5) up- or down-regulated • Of the 16,220 genes analyzed, 504 were up-regulated, and 224 were down-regulated Dissertation Proposal

11. Gene Expression Data • The data produced suggests: • Calcium homeostasis changes with age • ROS did not increase with age • Glycolysis activity increases with age • ATP and biosynthesis decrease with age • Inflammation and apoptosis-inhibiting genes increased with age • Many of these point to the possibility of a retrograde response defense mechanism, potentially mediated by the transcription factor Nf-ĸB (Giardina, 2002) Dissertation Proposal

12. Schematic Model Summarizing Gene Expression Data Dissertation Proposal

13. Fuzzy Modeling Approach • Modeling of cellular behavior can be done in great detail quantitatively (Kowald, 1996; Werner, 2005; Wallace, 2005) • To compare against gene expression data, which is statistically quite variable, a fuzzy logic approach is being used to assess qualitative behavior of cells (Center, 1998; Franco-Lara, 2007) • Allows larger scale models to be created from qualitative gene expression data (Nicholls, 2004) Dissertation Proposal

14. Fuzzy Modeling Approach • The model used for preliminary analysis is the Bionet tool (Bosl, 2007; Doi, 2004) • A Java-based application, it uses fuzzy logic to model cellular pathways • Developed by Dr. William Bosl of Harvard Medical School • Nodes often represent the quantity of a species, scaled from 0 to 1 in six fuzzy ranges (near zero, plus very low to very high) Dissertation Proposal

15. Fuzzy Modeling Approach • While the Bionet tool has been adequate for preliminary analysis of the Vicious Cycle and Retrograde Response, it is expected that a custom tool will be developed using Matlab Dissertation Proposal

16. Vicious Cycle Model • The Free Radical and DNA damage theories of aging both indicate that damage to the cell occurs and accumulates throughout life • That damage, whether from ROS or genetic disturbances, leads to an exponential decay in the body due to deterioration of the mitochondria Dissertation Proposal

17. Vicious Cycle Model Dissertation Proposal

18. ROS ATP biosynth Vicious Cycle Model Dissertation Proposal

19. Retrograde Response Model • In contrast, if a retrograde response is being activated in the cell, it should slow oxphos and increase glycolysis, in order to prevent ROS damage from accumulating, i.e. it’s a pro-survival mechanism • The increased activity of the transcription factor NF-kB with age is believed to be the major regulating mechanism for many intracellular processes Dissertation Proposal

20. Retrograde Response Model Dissertation Proposal

21. NF-kB ROS ATP biosynth Retrograde Response Model Dissertation Proposal

22. Fuzzy Modeling Goals • The goals of the fuzzy modeling portion of this research are to • Expand and refine the fuzzy models of cellular behavior to include other relevant processes, such as glycolysis, apoptosis, and inflammation • Refine modeling parameters (e.g. initial conditions, concentrations, organelle descriptors) based on experimental assays and published sources Dissertation Proposal

23. Network Theory of Aging • Biological pathways form networks, based on gene expressions which produce the species involved (Barabasi, 2004) • The diseasome maps which diseases are associated with the genes which may cause them (Goh, 2007) • The preliminary list of genes up- or down-regulated with age were cross-referenced with the diseasome Dissertation Proposal

24. Network Theory of Aging • Preliminary analysis identified 119 diseases, based on 81 genes • 22 genes were down-regulated, 59 up • Many of these diseases are strongly associated with increased age • For examples: deafness, diabetes, cardiomyopathy, hypertension, leukemia, gastric and colon cancers, ataxia, macular degeneration, and muscular dystrophy Dissertation Proposal

25. Network Theory of Aging • Goals for this portion of my research are to • Conduct more detailed investigation of the diseases associated with aging, as they relate to the connections with gene dysregulation • Supplement other gene expression changes with age, such as for brain, liver, and muscle tissue • Perform a pathway-based analysis by matching diseases and aging-related pathways Dissertation Proposal

26. Demographic Implications • The third portion of this research is looking for demographic evidence of the retrograde response • US Census data was obtained for death rates by single year age (Census, 2004) • From about age 30 on, an exponential increase in death rate should be seen • However perturbations about the exponential trend were seen Dissertation Proposal

27. Demographic Implications Dissertation Proposal

28. Demographic Implications • The residual between the log-linear regression and the actual death rate was calculated Dissertation Proposal

29. Demographic Implications • This shows a surprisingly cyclical behavior, with a period on the order of 160 years • It ends with a strong downturn in death rate, which agrees with observations of a plateau in death rate at ages 90+ (Vaupel, 1998; Weitz, 2001) Dissertation Proposal

30. Demographic Implications • Goals for the demographic aspect of this research are to • Further investigate trends in death rate at high ages • Find data for other developed countries and compare to US results • Determine if they support the hypothesis that the retrograde response is being activated • Investigate how diseases and chronic inflammation play a role in this behavior Dissertation Proposal

31. Summary This research uses changes in gene expression with age to support fuzzy logic and network modeling, then see if those results help explain biodemo-graphic trends Glenn Booker Dissertation Proposal 31

32. Credits • Thanks to • My advisor, Prof. Andres Kriete • Dr. Kriete’s team who conducted the gene expression studies (Nirupama Yalamanchili, William Beggs, Kelli Mayo, Ulrich Rodeck) • Team of Dr. Barabasi (Northwestern University) for data sharing • Dr. William Bosl (Harvard Medical School) for Bionet • My dissertation committee • Drs. Aleister Saunders (Bioscience), Aydin Tozeren (Biomed), Bahrad Sokhansanj (Biomed), Donald McEachron (Biomed), Longjian Liu (Public Health) • Questions? Dissertation Proposal