Ji Li, Ph.D. - US grants

[unreadable] DESCRIPTION (provided by applicant): Alterations in the heart that occur during the aging process result in decreased myocardial function and render it more susceptible to damage. A common cause of damage to the myocardium is ischemic injury. Until now, experimental evidence linking a decline in ischemic stress tolerance to alterations in specific stress signaling pathways has been lacking. Recently, we have found that the AMP-activated protein kinase (AMPK) signaling pathway plays an important role in limiting cardiac necrosis, apoptosis and dysfunction induced by ischemia/reperfusion, and aging-associated reduction in AMPK activity that may be an important contributing factor in the reduced mitochondrial function and dysregulated intracellular lipid metabolism associated with aging in skeletal muscles. The applicant hypothesizes that aging is associated with a decline in the ability of cardiac cells to activate this host response to acute ischemic injury, which contributes to a reduced tolerance to ischemic insults. We will test this hypothesis by addressing the following specific aims using hearts from young (4-6 months of age) and old (24-26 months of age) Fisher 344 rats and C57BL/6 mice: i) to examine whether aged heart displays impaired activation of upstream mediators of AMPK stress signaling by clinically important ischemia/reperfusion stress and to investigate the mechanisms responsible for this alteration in signaling. ii) to determine the effects of aging on the multifactorial downstream effectors of stress-induced AMPK signaling pathways in the ischemic heart, and to elucidate the role of stress signaling in impaired ischemic tolerance in aging. This aim will address whether defective AMPK activation with aging leads to reduced downstream signaling and increased susceptibility of the myocardium to ischemia/reperfusion injury. AMPK deficient (KD) transgenic mice and pharmacologic stimulation of AMPK will be used to demonstrate the important role of AMPK in maintaining ischemic tolerance. We also outline future experiments to examine the effect of modulating behaviors, namely caloric intake and exercise, on the AMPK signaling pathway in the aged heart, to elucidate the potential role of interventions that might lead to AMPK stimulation in managing cardiovascular disease in the elderly. Better understanding of the mechanisms leading to altered cardiac AMPK activation in response to ischemic stress with aging is important to fully understand the basis for increased susceptibility of the elderly to ischemic injury and could lead to therapeutic strategies aimed at limiting cardiac damage. [unreadable] [unreadable] [unreadable]

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Alterations in the heart that occur during the aging process result in decreased myocardial function and render it more susceptible to damage. A common cause of damage to the myocardium is ischemic injury. Until now, experimental evidence linking a decline in ischemic stress tolerance to alterations in specific stress signaling pathways has been lacking. Recently, we have found that the macrophage migration inhibitory factor (MIF)-AMP-activated protein kinase (AMPK) signaling pathway plays an important role in limiting cardiac damage and dysfunction induced by ischemia/reperfusion, and aging-associated reduction in AMPK activity that may be an important contributing factor in the reduced mitochondrial function and dysregulated intracellular lipid metabolism associated with aging in skeletal muscles. We hypothesize that aging is associated with a decline in the ability of cardiac cells to activate this host response (MIF-AMPK cascades) to acute ischemic injury, which contributes to a reduced tolerance to ischemic insults. These experiments will examine whether normalization of AMPK activation by MIF in the aged heart mitigates injury during ischemia/reperfusion. We outline future experiments to examine the effect of modulating behaviors, namely caloric intake and exercise, on the MIF-AMPK signaling pathway in the aged heart, to elucidate the potential role of interventions that might lead to AMPK stimulation in managing cardiovascular disease in the elderly. Better understanding of the mechanisms leading to altered cardiac AMPK activation in response to ischemic stress with aging is important to fully understand the basis for increased susceptibility of the elderly to ischemic injury and could lead to therapeutic strategies aimed at limiting cardiac damage.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Array comparative genomic hybridization (aCGH) allows identification of copy number alterations across genomes. The key computational challenge in analyzing copy number variations (CNVs) using aCGH data or other similar data generated by a variety of array technologies is the detection of segment boundaries of copy number changes and inference of the copy number state for each segment. In this subproject, we have developed a novel statistical model based on the framework of conditional random fields (CRFs) that can effectively combine data smoothing, segmentation and copy number state decoding into one unified framework. Our approach (termed CRF-CNV) provides great flexibilities in defining meaningful feature functions. Therefore, it can effectively integrate local spatial information of arbitrary sizes into the model. For model parameter estimations, we have adopted the conjugate gradient (CG) method for likelihood optimization and developed efficient forward/backward algorithms within the CG framework. The method is evaluated using real data with known copy numbers as well as simulated data with realistic assumptions, and compared with two popular publicly available programs. Experimental results have demonstrated that CRF-CNV outperforms a Bayesian Hidden Markov Model-based approach on both datasets in terms of copy number assignments. Comparing to a non-parametric approach, CRF-CNV has achieved much greater precision while maintaining the same level of recall on the real data, and their performance on the simulated data is comparable.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We study the haplotype inference problem from pedigree data under the zero recombination assumption, which is well supported by real data for tightly linked markers (i.e. single nucleotide polymorphisms (SNPs)) over a relatively large chromosome segment. We solve the problem in a rigorous mathematical manner by formulating genotype constraints as a linear system of inheritance variables. We then utilize disjoint-set structures to encode connectivity information among individuals, to detect constraints from genotypes, and to check consistency of constraints. On a tree pedigree without missing data, our algorithm can output a general solution as well as the number of total specific solutions in a nearly linear time O(mn . alpha(n)), where m is the number of loci, n is the number of individuals and alpha is the inverse Ackermann function, which is a further improvement over existing ones. We also extend the idea to looped pedigrees and pedigrees with missing data by considering existing (partial) constraints on inheritance variables.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. In this subproject, we implement a web application tool named MAVEN--for Management, Analysis, Visualization and rEsults shariNg of genome-wide association data using cutting edge technologies. Main capabilities include user data uploading and management, queries using a variety of criteria, visualization of results, interactive selections and seamless integration of users'data with databases at the National Center for Biotechnology Information (NCBI) for functional annotations of single nucleotide polymorphisms (SNPs) and genes. AVAILABILITY: http://cbc.case.edu/maven.

DESCRIPTION (provided by applicant): The overall goal is to elucidate the molecular and physiological mechanisms in the heart that promote cardioprotection against myocardial ischemia and ischemia/reperfusion (I/R) injury in the elderly. With aging, the ability of the myocardium to tolerate ischemic stress becomes compromised. Consequently, there is more morbidity and mortality in patients that are over 70 years of age receiving current interventions for myocardial infarction. Yet the mechanisms responsible for this age-related impairment in the adaptive response to I/R remains incompletely understood. Therefore, understanding the alteration of these mechanisms within the aging heart is fundamental for improving therapeutic strategies targeted against such cardiovascular pathologies. Our group and others have provided extensive evidence suggesting that activation of the AMP- activated protein kinase (AMPK) signaling pathway is highly advantageous to the heart. Moreover, we have recently demonstrated that during myocardial ischemia, AMPK activation is significantly impaired in the aged heart and that this is directly associated with increased myocardial infarction and cardiac dysfunction. However, how AMPK is activated during myocardial ischemia in addition to the endogenous mechanisms explaining the differences observed in impaired AMPK activation between young and aged hearts remains largely elusive. Recently, a novel group of proteins that lack kinase activity, known as the sestrins, particularly Sestrin2, have been demonstrated to increase the activation of AMPK in vitro and in vivo. Sestrin2 also limits cell death against hypoxic insults, limits oxidative stress, and increases the autophagic flux, all of which are important in age-related cardiac dysfunction. Accordingly, we hypothesize that Sestrin2 may be an integral part of the stress response that occurs during myocardial I/R and that its cooperation with the AMPK signaling pathway is altered with cardiac senescence. This hypothesis will be tested with two aims. First, we aim to define sestrin2 as a critical component of the adaptive response during I/R injury. Second, we aim to characterize how Sestrin2 is involved in the impaired AMPK signaling pathway during I/R in the aged heart. The proposed research takes an interdisciplinary approach encompassing physiologically relevant in vivo and ex vivo models of aging and I/R injury. In this manner, the proposed research will highlight new therapeutic targets and further our understanding about how specific stress-activated cardioprotective pathways are impaired with aging.