Coleen T. Murphy - US grants

07 Molecular and Cellular Biology Coleen T. Murphy, Ph.D. Slowing the Ticking Clock: C. elegans Screens for Reproductive Aging Regulators Human reproductive aging manifests itself in maternal age-related increases in infertility, miscarriage, and birth defects. We propose to develop methods to prevent and treat age- related reproductive problems. For this purpose, we have developed a C. elegans as a model of reproductive cessation, and we are using it to find mutants and chemical treatments that extend the reproductive period. The goals of our work are to (1) physiologically and molecularly characterize the cause of reproductive cessation in wild-type animals, (2) identify mutants that slow reproductive aging and maintain egg quality later in life, and (3) carry out a high-throughput screen for chemical compounds that slow reproductive aging. Thus far we have been able to determine the underlying cause of reproductive aging in C. elegans, decreased egg quality, which is also thought to be the underlying cause of human reproductive aging. Thus, our model has great potential to aid in the study of human reproductive aging. We have also identified a conserved TGF-ss pathway as a major regulator of reproductive aging, and have defined its downstream transcriptional effects. Finally, we have designed and carried out pilot screens to identify mutants with extended reproductive spans. In addition to the mutants we select in the screen, which represent possible new drug targets, we propose using a chemical genetic screen to identify candidate drugs for the treatment of age-related reproductive problems. Our screen will not only identify chemical compounds that can increase progeny viability, it will also determine the effect of these chemicals on the health of the mother. These approaches will expand our knowledge of the causes of reproductive aging, and will help identify candidates for the treatment and prevention of age-related reproductive decline.

DESCRIPTION (provided by applicant): C. elegans, like humans, experience cognitive functional declines with age, but the cause of these declines are not yet known. We propose to identify age-related changes in neuronal function, and to distinguish those changes that are functionally deleterious from those that may be an adaptive response to aging. In our first Aim, we will identify the genes required for long-term associative memory (LTAM) that change with age and with decreased function, and rescue function with age through manipulation of candidate genes. Our second Aim focuses on the identification of the cells involved in LTAM, and the characterization of their roles in the LTAM process. Furthermore, we will assess changes in cellular function with age. Finally, we will compare changes during normal aging to pathological changes in two C. elegans models of dementia. Comparisons with models of dementia will distinguish healthy from pathological age-dependent changes. Through these studies, the contributions of specific components to functional cognition will be used to identify the best targets of therapeutic intervention to treat cognitive decline with age. PUBLIC HEALTH RELEVANCE: In our work, we propose to use the model organism C. elegans to discover genes whose changes in function are correlated with decline in cognitive ability with age. We have designed a test of long-term memory in this organism, and observe that the animals lose their ability to remember with age. Using this test and various molecular tools, we can study the genes and cells responsible for loss of memory with age and in neurodegenerative disease.

? DESCRIPTION (provided by applicant): Reduced insulin/IGF-1-like signaling (IIS) extends C. elegans lifespan by up-regulating stress response (Class I) and down-regulating development (Class II) genes through a mechanism that depends on the conserved transcription factor DAF-16/FOXO. By integrating a genomewide analysis of gene expression responsiveness to DAF-16 with genomewide in vivo binding data for a compendium of transcription factors, we discovered that the transcriptional activator PQM-1 directly controls Class II genes by binding to the DAF-16 associated element (DAE). DAF-16 directly regulates Class I genes only, through the DAF-16 binding element (DBE). Loss of PQM-1 suppresses daf-2 and eat-2 longevity as well as thermotolerance, and further slows development. The nuclear presence of PQM-1 and DAF- 16 is controlled by IIS in opposite ways, and, surprisingly, was found to be mutually exclusive. We also observe progressive loss of nuclear PQM-1 with age, explaining declining expression of PQM-1 targets. Together, our data suggest an elegant mechanism for switching between stress response and development. The overall goal of this project is to elucidate the mechanisms underlying the observed antagonistic relationship between PQM-1 and DAF-16. We will employ high-throughput screens based on reporter assays and microfluidics microscopy to identify genetic and small-molecule regulators of PQM-1 translocation. Additionally, we will use mass spectrometry to identify PQM-1's post-translational modifications and protein interactors, and determine how these affect nuclear translocation. We will also identify factors responsible for the nuclear exit of DAF-16 and PQM-1 with age. Finally, we will identify PQM-1 homologs in mammalian cells that exhibit a similar antagonism with FOXOs. Together, our results and insights will provide a framework for understanding how PQM-1 and DAF-16 and its mammalian counterparts allow cells to strike a balance between development and stress response.

? DESCRIPTION (provided by applicant): The aging of neurons causes dysfunction and cognitive decline, but exactly how neurons age is not yet understood. In particular, the key genes that are responsible for these changes have not been identified, but would be ideal therapeutic targets if found. Our hypothesis is that a subset of the genes that change with age in specific neurons is responsible for changes in declines in cognitive ability with age. Our work identifying gene expression changes in aging adults and in longevity mutants that maintain cognitive functions longer will allow us to identify these key genes. These regulators, if evolutionarily conserved, may be good targets for intervention if they also decline with age in human neurons. In our previous studies, we developed assays to measure C. elegans positive olfactory learning, short-term memory, and long-term memory. We found that the molecular components of these processes are shared between worms and mammals, demonstrating that C. elegans is a good model system to more fully understand the molecular and cellular requirements of memory. Further, we assessed the changes in learning, short-term memory, and long-term memory with age, in longevity mutants, and in models of Alzheimer's Disease. We found that levels of the transcription factor CREB limit long-term memory and fall with age, explaining the loss of memory ability with age. We went on to identify CREB's downstream targets required for memory, as well as the neuronal site of CREB activity, extending the knowledge of CREB's activity beyond what is known in other systems. However, how other behaviors are limited with age is not yet understood at the molecular level, and we aim to identify key factors that regulate the maintenance of cognitive function with age. In order to refine our analyses, we have developed a novel method to isolate cells from adult C. elegans, allowing transcriptional analysis of single cell types in aging worms for the first time. We are leveraging that new technique to identify genes that change with age and in longevity mutants in different neuron types. In addition to obtaining the basal transcriptome for individual cell types n order to characterize their identities, we can now assess their individual transcriptional changes with age. We have also utilized longevity mutants with extended functions, allowing us to identify key genes that maintain function with age. This is a key tool that is uniquely available i C. elegans. The effect of these changes can then be assessed through tests of motility, chemotaxis, learning, memory, regeneration, and morphology with age. The proposed experiments will use our newly developed methodology to determine how neurons lose the ability to carry out specific functions with age. Further, we will combine neuron-specific rescue o these key genes with behavioral assays to determine their roles and test whether their activity is sufficient to prevent specific behavioral declines with age. This information will give us unprecedented resolution in identifying causative changes in neurons with age.

? DESCRIPTION (provided by applicant): Multi-cellular organisms face the challenge of coordinating all of their tissues' functions in response to changing nutrients, temperatures, and environments for the benefit of the whole organism. Disease and aging also have effects that are both tissue-specific and systemic. However, the question of how tissues are coordinated throughout a whole organism is currently an unsolved problem. The nematode C. elegans has a simple body plan, with only 959 cells and a small number of major tissues. While some tissues have been well studied, we know less about others, and it is becoming appreciated that some of these lesser-studied tissues have endocrine (hormonal signaling) functions. Specifically, recent evidence suggests that the worm's skin (hypodermis) and intestine are major endocrine tissues, coordinating signals from the neurons about nutrients and conditions, and translating that information into decisions about longevity and reproduction. In our previous work, we found that reproductive aging and somatic aging rates are determined non-cell autonomously. However, the relevant tissues are relatively uncharacterized, due to the difficulty in isolating adult C. elegans tissues. My lab recently solved this problem, developing a method to gently dissociate adult C. elegans tissues, allowing us to sort cells and perform RNA-seq to identify the transcriptome of each tissue type in the animal. In this project, we will use our technique to obtain tissue-specific transcriptome information for every tissue (the tissueome) and couple that information with computational approaches to identify networks of activity and communication. We will also use biochemical methods to determine tissue-specific transcription factor activity, which will allow us to understand how C. elegans integrates signals to convey metabolic and longevity decisions to the whole animal. C. elegans' small number of cells and simple tissues make it an ideal system in which to not only

PROJECT SUMMARY Transgenerational epigenetic inheritance (TEI) has been observed in worms, flies, and mice, and proposed in humans (e.g., Dutch Hunger Winter), but the underlying and regulatory molecular mechanisms are largely unknown. Similarly, we do not yet understand how ubiquitous trans-kingdom signaling between pathogens and hosts is. Therefore, it is critical to study these mechanisms in model systems. We recently discovered that the nematode C. elegans, which both eats and is infected by bacteria, can survey its environment, detect and learn to avoid pathogens, and then pass this information on to four generations of its progeny (Moore, et al., Cell 2019); we propose that this is a nascent form of adaptive immunity. Well-conserved molecular processes (RNA interference, COMPASS histone modification, piRNAs) across several tissues (intestine, germline, and neurons) are required to alter behavior in response to Pseudomonas aeruginosa (PA14). Worms read small RNA bacterial signals, interpret this information as a predictor of future infection, and transmit the information to alter behavior by downregulating a neuronal gene with complementary sequence (Kaletsky, et al. BioRxiv 2020; Kaletsky et al. Nature, in press). How is the sRNA signal conveyed from the germline to neurons? We found that the Ty3/Gypsy retrotransposon Cer1 is required for learned pathogenic avoidance, TEI, and survival on PA14. This is paradigm shifting: conventional wisdom holds that retrotransposons are deleterious, and that piRNAs are critical to repress these genomic parasites. Our results instead suggest that Cer1 may have been selected to fight against the most abundant pathogens in C. elegans' environment. We hypothesize that Cer1 forms vesicle- like particles that carry sRNAs to neurons. Proposed experiments will characterize the nature of the germline-to- neuron signal, determine the evolutionary conservation of the mechanism, and determine how the transgenerational ?clock? is sett. Because the molecular components we have already observed are conserved, our results will identify candidate molecular requirements for TEI in other animals.

The rise in antibiotic resistance has severely depleted our arsenal for combatting deadly bacterial pathogens. Meanwhile, despite increased appreciation of the myriad ways that microbiome bacteria impact human health, most of the signals that bacteria use to influence hosts remain unknown. This proposal seeks to address both of these challenges by leveraging our team?s unique expertise and recent discovery that animals can directly sense and respond to bacterial small RNAs (sRNAs). Since the discovery of antibiotics in the 1920s, the pathogenesis field has primarily focused on small molecules: nearly all known antibiotics and bacterial signaling molecules are small molecules. But we sorely need new, orthogonal approaches. Nucleic acid-based therapies have emerged as an exciting new platform for rapid drug development. Due to their chemical similarity, the pharmacology of nucleic acids is established, such that once we know what sequence to target, the drug development pipeline is relatively streamlined (at least in comparison to small molecule drugs). For example, a Batten disease patient was recently successfully treated with a personalized synthetic antisense RNA, less than a year after her genome was sequenced. RNA-based interventions have typically not been considered for bacteria because bacterial RNAs were thought to function exclusively within the bacteria. However, we recently overturned this paradigm by proving that model animal hosts can directly ?read? the sRNAs produced by the human pathogen, Pseudomonas aeruginosa, using the RNA-interference (RNAi) machinery to respond to the bacterial sRNAs. This result is particularly exciting because it suggests a previously unappreciated role for the RNAi machinery in sensing and responding to bacteria. It also suggests that understanding sRNA-based microbe-host signaling could help develop new therapies to help hosts ward off pathogens or promote commensal colonization. However, advancing such new antimicrobial strategies is currently hindered by our lack of knowledge regarding the space of sRNA-mediated bacteria-host interactions and the molecular mechanisms by which they function. Here, we propose to build off our discovery of sRNA-host signaling to significantly close this knowledge gap. This will be accomplished in three complementary parts that span multiple hosts and microbes: globally mapping human gut microbiome community sRNA-host interactions and functions, determining how mammalian cells respond to pathogen sRNAs, and using C. elegans to characterize the molecular mechanisms of sRNA-host interactions. To achieve these goals we will combine the expertise of our team, comprised of leaders in the fields of human microbiome and computational biology (Donia), microbial pathogenesis and antibiotic development (Gitai), and C. elegans behavior and genomics (Murphy). Our combined efforts thus have the potential to establish new paradigms for microbe-host interactions and pave the way to desperately-needed new therapies.