2001 — 2003 |
Kennedy, Scott Garwood |
F32Activity Code Description: To provide postdoctoral research training to individuals to broaden their scientific background and extend their potential for research in specified health-related areas. |
Neuronal Signal Transduction in C Elegans @ Massachusetts General Hospital
DESCRIPTION: The study of dauer formation in C. elegans has been instrumental in our understanding of both the insulin and TGFB signaling pathways. It is my intent to use C. elegans to identify neuronal signaling molecules involved in the regulation of these neuroendocrine outputs. Preliminary experiments have identified cyclic GMP and cyclic GMP regulated ion channels as being important for regulation of dauer formation. Here I present additional genetic and genomic experiments which aim to uncover the mechanism(s) of cGMP and CNG channel regulation of neuroendocrine outputs in the genetic model organism C. elegans. Given the prominent role that ion-channels play in signal processing it is not surprising that many inherited human diseases are the results of mutations in channel genes (channelopathies). It is my hope that these studies will unveil the identity and function of additional evolutionarily conserved neuronal signaling molecules that may increase our understanding of the pathologies of these diseases.
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0.907 |
2005 — 2009 |
Kennedy, Scott G |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Regulation of Small Rnas by the Eri-1 Genetic Pathway @ University of Wisconsin-Madison
Exposure of many organisms to double-stranded RNA causes the degradation of mRNA molecules containing sequences homologous to the trigger dsRNA, a process termed RNAi. Genetic and biochemical analysis in model organisms, such as C. elegans, has demonstrated that much of the mechanistic underpinnings of RNAi are evolutionary conserved. Many fundamental questions remain to be addressed in the RNAi field including: (1) What are the endogenous biological functions of the RNAi machinery;and (2) Is RNAi, like most biological processes, under negative regulation? We have undertaken a genetic screen seeking to identify negative regulators of RNAi. These studies have thus far led to the characterization of the gene eri-1. Our results suggest that ERI-1 functions to negatively regulate R;NAi by degrading the small RNA executioners of RNAi (siRNAs). We have now begun to characterize four additional genes which function in a genetic pathway with eri-1 (termed the eri-1 pathway). Our preliminary data suggests that the eri-1 pathway proteins function in a complex with the C. elegans Dicer-like protein DCR-1 to regulate siRNA stability. Finally, our data indicate that the eri-1 pathway proteins are required for a novel mode of gene regulation, a process we term endogenous RNAi. This proposal seeks to: (1) characterize the molecular function of ERI-1 in detail;(2) continue our genetic analysis of the eri-1 pathway genes;and (3) elucidate the role of the eri-1 pathway genes in the biogenesis and function of small RNAs in C. elegans. Initial successes utilizing siRNAs to target oncogenic and viral proteins have generated excitement that siRNAs may eventually be utilized to treat human disease. Understanding the endogenous biological activities of small RNAs and how these small RNAs are generated and regulated is essential prior to the rationale use of siRNAs in treating human disease.
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0.901 |
2009 — 2021 |
Kennedy, Scott G |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Small Regulatory Rna Functions in the Nucleus
PROJECT SUMMARY Epigenetics is the study of changes in gene expression or phenotypes that are not the result of changes in DNA sequence. RNA has emerged as an important informational vector directing many epigenetic processes. Additionally, for most of the last century it was widely believed that (unlike genetic information) epigenetic information did not pass across generational boundaries. In other words, epigenetic information was erased each and every generation such that offspring began life with a blank epigenetic slate. It is now known that this is not always the case. Many examples of the trans-generational transfer of epigenetic information have now been documented. The inheritance of epigenetic information for more than one generation is termed transgenerational epigenetic inheritance (TEI). Non-coding RNAs and, in particular, small non-coding RNAs such as piRNAs, miRNAs, siRNAs, and tRNAs have now been linked to TEI in plants, worms, insects, and mammals. Thus, small non-coding RNAs are important informational vectors for TEI in many eukaryotes. In most eukaryotes, dsRNA induces gene silencing (RNAi). We have used RNAi in C. elegans to identify factors that couple small non-coding RNAs to transcriptional regulation. Recently, these studies led us to discover a new type of silencing RNA that we term the pUG RNA. Amazingly, progeny of C. elegans subjected to RNAi inherit the ability to silence RNAi-targeted genes for many (5-10) generations (termed RNAi inheritance). Thus, RNAi inheritance in C. elegans is a particular robust example of RNA-directed TEI. We are also using RNAi inheritance in C. elegans as a model system to explore the mechanistic underpinnings of RNA-directed TEI in animals. We are using genetic screens to identify cellular factors required for promoting and limiting TEI and biochemical and cell biological approaches to explore how these factors drive TEI. Finally, we are also using this system to explore why animals have TEI systems in the first place. The evolutionarily conserved connections between non-coding RNAs and TEI processes in many different species suggests that the work we are doing in C. elegans may lead to fundamental insights into mechanisms of TEI, which will be applicable to eukaryotes in general. The mis-regulation of epigenetic pathways is known to contribute to the etiology of dozens of human diseases, including cancer. Our proposed work will likely increase our understanding of how RNA reprograms epigenetic states and, therefore, may help us understand and, possibly, treat these diseases. Additionally, the question of whether or not people can inherit epigenetic information from their parents is the subject of intense scientific debate. If people can indeed inherit epigenetic information from their parents then it stands to reason they could inherit the wrong epigenetic information, which might predispose to disease. Our work exploring mechanisms of RNA-directed TEI may make it possible to influence TEI pathways in people to mitigate disease.
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1 |
2013 — 2016 |
Kennedy, Scott G |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Multi-Generational Epigenetic Inheritance and Germline Immortality
DESCRIPTION (provided by applicant): Epigenetics is the study of changes in gene expression or phenotype that occur without associated changes in DNA sequence. Epigenetic processes drive and/or regulate a wide-variety of biological processes such as imprinting, X-chromosome inactivation, and paramutation. Epigenetic information can be inherited across generational boundaries. A particularly striking example of epigenetic inheritance is dsRNA mediated gene silencing (RNAi). In C. elegans gene the effects of RNAi can persist for more than ten generations; a process termed RNAi inheritance. The following questions concerning RNAi inheritance have not been answered. What is the molecular agent that drives RNAi inheritance? How are non-coding RNA- directed epigenetic memories maintained across generations? Are genes normally subjected to heritable epigenetic regulation during reproduction? If so, why? Our long-term goal is to answer these questions. Towards this goal, we have conducted a genetic screen in C. elegans designed to identify cellular factors specifically required for inheritance of dsRNA-mediated silencing signals. This screen identified at least four genes including the gene failure to inherit RNAi (finn)-1. finn-1 encodes an Argonaute (Ago) that associates with siRNAs, and promotes RNAi inheritance, in germ cells of the progeny of animals exposed to dsRNA. Under normal growth conditions, FINN-1 associates with endogenously expressed small RNAs, which direct chromatin modifications in germ cells. In animals lacking FINN-1, these chromatin marks are lost over generations, and, concomitantly, these animals become sterile due to multi-generational atrophy of the germline. These results establish that small RNAs, acting in conjunction with FINN-1, are required for RNAi inheritance and germline immortality. In this proposal, we seek to identify additional components of the RNAi inheritance machinery and explore in more detail how FINN-1 and small regulatory RNAs direct RNAi inheritance and germline immortality. Our experiments are revealing how and why non-coding RNAs drive epigenetic inheritance. Non-coding RNAs are associated with a diverse array of epigenetic phenomena. Therefore, we believe that insights from our research will prove to be globally applicable to our understanding of epigenetic inheritance in animals. In addition, mis-regulation of epigenetic pathways in humans contributes to disease. Thus, the knowledge we provide might make it possible to influence epigenetic processes with the goal of mitigating human disease.
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1 |
2019 — 2021 |
Kennedy, Scott G |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Spatiotemporal Regulation of Liquid-Like Condensates in the Germline
SUMMARY/ABSTRACT Liquid droplet organelles (also referred to as liquid-like condensates) are dynamic concentrations of protein and RNA that coalesce spontaneously from the cytoplasm or nucleoplasm via liquid-liquid phase transition. Like oil and water, these liquid droplets and their surrounding cytoplasm are thought to co-exist as separate states of liquid. Current models posit that liquid droplet organelles may exist to concentrate reactants together in space and time in ways that facilitate biochemical reactions such as the complexes processes that underlie gene regulation. Eukaryotic cells possess many non-membrane-enclosed liquid droplet organelles including nucleoli, processing bodies, cajal bodies and germ granules. Germ granules are found in the germ cells of all/most animals where they are thought to contribute to germ cell totipotency. Indeed, orthologous proteins (e.g. VASA) are found in germ granules of many different species of animals, hinting that some aspects of germ granule function may be conserved in all animals. Most epigenetic information is erased at or near the start of each new generation in animals to ensure totipotency of the germline. In some cases, epigenetic information escapes reprogramming and is passed from parent to offspring. The inheritance of epigenetic information for more than one generation is termed trans- generational epigenetic inheritance (TEI). Small non-coding RNAs (e.g. siRNAs, miRNAs, piRNAs, and tRNA fragments) have emerged as important mediators of TEI (cumulatively, RNA-directed TEI). dsRNA-mediated gene silencing (RNAi) in C. elegans is a robust and dramatic example of RNA-directed TEI. My lab is using RNAi inheritance in C. elegans as a model system to explore how epigenetic signals are passed across generations in animals. We recently conducted a genetic screen for RNAi inheritance factors that identified two conserved RNA binding proteins (RBPs). These RBPs contribute directly to inheritance by helping to maintain the expression of silencing RNAs over generations during RNAi inheritance. Interestingly, both RBPs localize to a new C. elegans germ granule whose biogenesis is developmentally regulated and whose positioning relative to other germline condensates is highly ordered. Finally, we find that the two RNAi inheritance factors we have identified are required for maintaining germline immortality. Together, our results have led us to propose that the temporal and spatial ordering of liquid droplet organelles may help germ cells organize and coordinate the complex RNA processing pathways underlying gene regulatory systems, such as RNA-directed TEI and germline immortality. This proposal outlines our efforts to further understand how liquid-like condensates form during development, how they assemble into complex structures with other germline condensates, and, most importantly, why they do so.
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1 |
2019 — 2020 |
Kennedy, Scott G |
R21Activity Code Description: To encourage the development of new research activities in categorical program areas. (Support generally is restricted in level of support and in time.) |
Transgenerational Inheritance of Protein Aggregates in Animals
PROJECT SUMMARY / ABSTRACT Protein-based inheritance is known to occur in yeast, where prions can adopt self-replicating structures. Recently, proteins containing intrinsically disordered regions (IDRs), or regions that lack a well-defined three- dimensional structure, were also shown to mediate inheritance in yeast (Chakrabortee et al. 2016). It is unknown whether prions or IDR proteins can mediate inheritance in animals. While studying the role of IDR proteins in dsRNA-mediated gene silencing (RNAi) in C. elegans, we made the following unexpected observation. In particular genetic backgrounds, the C. elegans IDR protein PGL-1 forms aggregate-like structures in germ cells. Amazingly, these PGL-1 aggregates are maintained in the germline (inherited) by animals for multiple generations after these animals no longer possess the mutation that originally triggered their formation. These data have led us to hypothesize that IDR proteins can form self-propagating aggregates in animals and thereby mediate transgenerational inheritance. This proposal uses C. elegans as an animal model system to test this central hypothesis, as well as explore, more generally, the incidence and consequence of heritable protein structures that occur in animal germlines. Interestingly, many IDR proteins form aggregates in the context of human disease. IDR protein aggregates are associated with proteinopathic diseases such as Alzheimer's, ALS, and Parkinson's disease. The pathological consequences of protein aggregation are widely believed to be limited to a single generation: Known protein aggregates form in aging somatic tissues, and the soma is not passed to progeny. This seeming constraint might be overcome, however, if a self-propagating protein aggregate were to form in the germline. Every animal (and every animal cell) alive today is directly related to germ cells that existed many millions of years ago. Thus, if self-propagating protein aggregates were to form in a germ cell, those aggregates might be passed from generation to generation, leading to long-term deleterious and heritable consequences. Therefore, we speculate that protein-based inheritance might explain some of the heritability of proteinopathies that remains unaccounted for to date. Our long-term goals are to determine the extent to which protein-based structures mediate inheritance in animals, and, ultimately, ask if and how structure-based inheritance contributes to the inheritance of disease in humans. This proposal is innovative because it describes the first example (that I am aware of) of a heritable protein aggregate (protein-based inheritance) in animals. This proposal is significant because it will likely advance our understanding of two important, yet poorly understood, areas of biology: protein aggregation and non-Mendelian transgenerational inheritance. Finally, the proposal is significant because the work we are doing may impact our understanding of the etiology and possibly the treatment of diseases such as human proteinopathic disorders.
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1 |
2020 |
Kennedy, Scott G Winston, Fred M. [⬀] |
T32Activity Code Description: To enable institutions to make National Research Service Awards to individuals selected by them for predoctoral and postdoctoral research training in specified shortage areas. |
Genetics and Genomics Phd Training Grant
The T32 Program in Genetics and Genomics at Harvard Medical School trains 6 student per year to prepare them for careers advancing our understanding of the fundamental mechanisms of hereditary disease, and genomic methodologies. This is a proposal for a supplement that will allow us to develop new programming that advances diversity of our students, and promotes a sense of inclusion across the program. The proposal is designed to develop and test programs that can, if successful, become part of the orientation activities and coursework for all of the PhD students in life sciences at Harvard Medical School. To do so we will 1) develop novel orientation events that will establish an inclusive culture and community, and will involve both incoming students and more senior members of the community 2) work with Diversity Fellows from the School of Education to initiate new programming focused on sustaining inclusive learning environments in the lab, activities that can be incorporated into the ongoing Conduct of Science course, and 3) host a Symposium on Bias in Genetics and Genomics Research, to demonstrate the importance of diversity and inclusion in our science, as well as in our new scientists. These activities are designed to enhance the training program in genetics and genomics and extend the impact of these efforts to the broader HMS community and scientific community.
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1 |
2021 |
Kennedy, Scott G |
T32Activity Code Description: To enable institutions to make National Research Service Awards to individuals selected by them for predoctoral and postdoctoral research training in specified shortage areas. |
Program in Genetics and Genomics Phd Training Grant
Abstract: This is a new application to support twelve graduate students in their second year of a Ph.D. Program in Genetics and Genomics (PGG) at Harvard Medical School (HMS). Scientists in the fields of genetics and genomics are at the forefront of our Nation?s efforts to understand how life works and to diagnose and treat human disease. The mission of PGG is to provide a diverse group of students with the intellectual, technical, and professional training that they will need to become future leaders in the fields of genetics and genomics. Training derives from a customized curriculum, which emphasizes rigor and reproducibility in research, technical training, training in scientific communication, professional networking, industry internship opportunities, and, of course, dissertation research. PGG students carry out Ph.D. research in one of forty laboratories centered around, but not exclusive to, the Department of Genetics at HMS. Laboratories of training faculty are well-funded and study a wide range of topics in the fields of genetics and genomics, which range from prokaryotic gene regulation to human biology and disease. Students supported by the training grant are part of the Biological and Biomedical Sciences (BBS) program at HMS, which is a large umbrella program that draws in a top group of graduate students each year. PGG provides a self-selected group of BBS students with the opportunity to be part of a close-knit community focused on technical and professional training in the area of genetics and genomics. PGG students are required to concentrate their course work in the fields of genetics and genomics, including a requirement to take at least one course in the quantitative analysis of biological data, and one course overtly covering the need for rigor and reproducibility in modern biomedical research. PGG students also participate in a set of programmatic activities, including (1) an annual symposium, (2) attend and present at student-led monthly research presentations, 3) networking opportunities with like-minded senior students and postdocs, including those studying clinical genetics, and (4) hosting outside genetics or genomics-oriented scientists for seminars. Students will be guided in courses and rotation selections by Program Advisors and by Dissertation Advisory Committees (DAC), which will include PGG trainers. Student progress will be monitored via course grades, PA evaluations, DAC updates, G3 research talks, and by faculty attendance at student seminars in the Genetics Department Data Club series. PGG curriculum and policy will be guided by evidence-based teaching approaches incorporated into curriculum, by course and program evaluations, and by a Steering Committee composed of PGG trainers and senior PGG students. Together, the training plan will give PGG students the skills they need to become leaders in the fields of genetics and genomics and to lead future efforts using the genetics and genomic sciences to promote human health.
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