Tim Schedl - US grants

The specification of germ cells to develop as sperm or oocyte is a process that is fundamental to all sexually reproducing metazoans. I am focusing on two genes that control germline sex determination in Caenorhabditis elegans, fog-2 and oop-1. The goal is to understand at the genetic and molecular level how these genes specify germline sexual fate. My genetic analysis has revealed that fog-2 is regulated in a temporal, germline specific, and sex specific manner. In turn, fog-2 regulates sex determination genes downstream in the pathway in specify spermatogenesis in the hermaphrodite germline. The proposed molecular analysis of fog-2 will provide basic information about the structure and expression of the fog-2 gene and distribution of the gene product. Such information will reveal if fog-2 is regulated at the level of RNA or protein accumulation. Genetic models for how fog-2 regulates downstream sex determination genes will be tested in vivo with a fog-2 mRNA microinjection assay. I have isolated mutations that define a new locus, oop-1 which controls the diverse germline processes of sex determination, proliferation and gametogenesis. One allele has a recessive germline tumorigenic phenotype. The proposed genetic analysis of oop-1 will reveal the range of processes that it controls and allow me to determine whether the oncogenic phenotype is a consequence of loss-of-gene-function or a rare mutant activity. Proposed molecular analysis will provide information about the structure of oop-1 and its possible relationship to genes that control proliferation and development in other eukaryotes. The health relatedness of the proposed work is two-fold. First, research on development in simple, experimentally accessible, metazoan systems as C. elegans provides information about fundamental processes that are involved in development of all animals, including humans. Second, our knowledge about genes in which recessive mutations cause neoplasia is rudimentary. Analysis of oop-1 offers the possibility that it will provide clues about such "recessive oncogenes" that may be applicable to human cancer.

9506220 Schedl Arrest of the cell cycle in prophase of meiosis I is a conserved feature of oogenesis in essentially all multicellular animals. Oocytes in organisms from starfish to humans maintain this arrested state until ovulation by a mechanisms that is not well understood. This proposal introduces a genetic strategy for isolating and characterizing molecular regulators of meiotic prophase cell cycle arrest. Recent genetic screens performed in the nematode Caenorhabditis elegans have identified mutants where oocyte arrest in diakinesis of MI prophase fails to be maintained. In oar-1 and oar-2 mutants (oar= oocyte meiotic prophase arrest defective), oocytes leave arrest and endomitotically replicate their DNA. Strategies have been developed to distinguish Oar mutants from other mutants producing endomitotic oocytes. Importantly, a mutant has been obtained with a phenotype opposite to Oar; olk-1 (olk= oocyte arrest lock) oocytes maintain arrest under conditions when arrest is usually lost. It is likely that the pathway for maintenance of meiotic arrest defined by the oar and olk genes involves cell cell communication from the soma to the oocyte. Analysis of oar-1 is consistent with the conclusion that a cell cell signal is needed to maintain meiotic arrest; cloning reveals that oal-1 encodes a Sec61p gamma protein known in other systems to facilitate protein translocation into the ER, and mosaic analysis shows oar-1 activity is needed specifically in the germline to prevent loss of oocyte arrest. Oar-1 may therefore act to translocate a transmembrane receptor to the oocyte surface for reception of the arrest signal. This proposal will initiate a more extensive genetic and molecular investigation of the pathway maintaining oocyte meiotic prophase arrest in C. elegans. Dr. Schedl will:1) Identify genes necessary for oocyte meiotic prophase arrest using a genetic screen, 2) Genetically and phenotypically characterize mutants in the oar collection, and 3) Genet ically characterize the arrest "loc-1" mutant, olk-1. ***

The proposed research uses the genetic analysis of C. elegans to address two fundamental questions in germline development: how is the decision to either proliferate or enter the meiotic pathway executed? And how are meiotic prophase progression and gametogenesis controlled and coordinated? Disruption of these processes can result in germline tumor formation, sterility and aneuploid gemetes. We have identified mutations that cause germline tumorigenesis by two different mechanisms. Gain-of- function mutations in the glp-I and let-42 genes lead to tumorigenesis by preventing germline stem cells from exiting mitosis and entering the meiotic pathway. In contrast, loss-of- function mutations in the gld-I gene cause tumor formation by disrupting meiotic prophase progression and oogenesis. In animals lacking gld-1 activity, germ cells that would normally develop into oocytes enter and progress through meiotic prophase normally until the early pachytene stage, when they exit the meiotic pathway and return to a proliferative cell cycle. We have shown that this return to mitosis is dependent on the activity of MAP kinase. We have also identified a new gene, pex-2, that is important for meiotic prophase progression. glp-1, let-42 and gld-1 are evolutionarily conserved. GLP-1 is related to the Notch family of receptors, which includes the human TAN-1 proto-oncogene product. Let-42 shows similarity to an uncharacterized human cDNA. GLD-1, a putative RNA binding protein, shares homology with the mouse Quaking protein and the human Sam68 protein. The specific aims of this proposal are to: A) identify genes that negatively regulate mitosis or positively regulate entry into meiosis by screening for enhancers of a weak glp-1 (gf) mutation; B) analyze the normal role of let-42 in germline proliferation; C) identify regulators, cofactors and RNA targets of GLD-1 and investigate the role of the MAP kinase pathway in germline tumorigenesis; and D) determine how pex-2 promotes meiotic prophase progression. The proposed studies relate to general aspects of biology and medicine. They will provide insights into: the regulation of mitosis; the control of entry into and progression through meiotic prophase; and the functioning and regulation of Notch family receptors, the MAP kinase signalling pathway, LET-42 and the GLD-1/Quaking/Sam68 subfamily of RNA binding proteins. This work may also provide new information about the cellular mechanisms that underlie human germline cancers.

AWARD ABSTRACT - 9818013
Confocal Microscope for Developmental Studies - Skeath et al.

This award supports the purchase of a laser-scanning confocal microscope to follow protein expression in living as well as fixed cells, tissues, and developing organisms. With this new microscope, researchers at Washington University will be able (i) to slice thin optical sections through thick fluorescent specimens; (ii) to view simultaneously the sub-cellular localization of three different molecules within such specimens; (iii) to follow in vivo the expression and localization dynamics of multiple proteins; (iv) to visualize specimen planes parallel to the light path; and, (v) to obtain high resolution 3-D views of all specimens. The microscope will expand the experimental techniques presently employed by the faculty at Washington University in St. Louis. The proposal details five projects where the new confocal microscope will have a major impact. These projects include: (i) analyzing the developmental and molecular mechanisms that control the generation of cell diversity in the central nervous system of the Drosophila embryo; (ii) understanding how interactions between the cytoskeleton and related components drive morphological changes in epithelia using the Drosophila eye as a model system; (iii) tracking the transcriptional regulation and function of muscle-specific genes in mammalian cell lines and mouse embryos; (iv) determining how germ cells regulate their decision to enter, and their progression through, the meiotic pathway; and, (v) elucidating the molecular mechanisms that control fin regeneration and pigment patterning in the zebrafish, D. rerio. A primary scientific and educational goal of the acquisition of a confocal microscope is to train researchers in the use of one of the most powerful microscopes used in the life sciences, so that these researchers may integrate the capabilities of a confocal microscope with their research. To facilitate maximum utility of the microscope, two of the principal investigators together with a representative from the confocal manufacturer will carry out training sessions on a monthly basis or as demand dictates. These sessions will ensure proper training for those who use the microscope. In this way, the PIs hope to make the confocal accessible to any interested party at the university, including post-doctoral researchers as well as graduate and, hopefully, undergraduate students.

This project will identify gene products that function in the free-living roundworm C. elegans germline development which are phosphorylation targets of MPK-1 ERK MAP Kinase. ERK MAP kinases act at the end of numerous extracellular signaling cascades, such as receptor tyrosine kinase pathways, which have essential functions in animal development and homeostasis. In many cases, the downstream target proteins that are activated or inactivated when phosphorylated by extracellular signal-regulated kinase (ERK) are unknown. In the model experimental organism C. elegans, there is a single gene similar to ERK (ERK ortholog) and is known as MPK-1. This functions in ten different germline processes and the target proteins that are phosphorylated by MPK-1 ERK to mediate these germline processes are unknown. In this project, a three-part approach will be used to identify MPK-1 ERK phosphorylation targets that function in germline development. In the first part, docking site sequences will be used to computationally identify C. elegans proteins that are potential targets of MPK-1 ERK phosphorylation. In the second part, in vivo validation of the predicted target gene products will be performed by RNA mediated interference of the corresponding genes in genetic backgrounds that are sensitized for MPK-1 ERK signaling. In the third part, selected in vivo validated targets will be confirmed as targets by in vitro phosphorylation using purified mammalian ERK. The Broader Impact of this project is at three levels: First, the project will provide research training in genetics, genomics and developmental biology for a postdoctoral fellow and a number of undergraduate students. Second, novel genes that mediate ten different aspects of germline development that are directly regulated by ERK will be identified. Third, given the conservation of both ERK signaling and germline development, it is very likely that the ERK targets identified in C. elegans will also be ERK targets in other animals.

DESCRIPTION (provided by applicant): Tissues are formed and maintained by stem cells that produce both daughters that undergo self-renewing proliferation and daughters that differentiate. The mechanisms by which the choice between proliferation and differentiation are made are not well understood in any system. Our long-term goal is to understand how the proliferation vs. differentiation decision is made in the C. elegans germline. The GLP-1 /Notch signaling pathway induces germ cells to proliferate while GLD-1, a conserved translational represser RNA binding protein, is a key downstream differentiation factor that promotes meiotic development. Spatial control of both GLP-1/Notch signaling and GLD-1 accumulation determines the correct balance between proliferation and meiotic development in C. elegans. Notch signaling in mammals is also important in stem cell self-renewal and oncogenic Notch activation can lead to cancer. The goal of Aim 1 is to identify and characterize negative regulators of GLP-1/Notch signaling that function to limit the size of the proliferative germ cell population. Mechanisms by which Notch signaling is down-regulated are not well understood but are of general importance since there are a number of developmental contexts where activated Notch proteins must be cleared between successive rounds of Notch mediated cell fate specification (e.g. nervous system). Aim 2 employs cell biological approaches to understand how GLP-1/Notch signaling controls proliferation over a distance of 20 cell diameters. The rise in GLD-1 levels, which is regulated by both translational activators and repressors, determines where germ cells enter meiosis and in Aim 3, additional gene products necessary for this control will be identified and characterized. In Aim 4, mRNA targets of GLD-1 that mediate initiation of meiotic development will be identified and characterized. GLD-1 likely translationally represses these RNAs to promote meiotic development. Since little is known about activities that lead to entry into meiotic prophase in animals, results from this aim will provide an initial picture.

[unreadable] DESCRIPTION (provided by applicant): ERK (extracellular signal regulated kinase) is the terminal kinase of a number of signaling cascades that regulate animal development and is often inappropriately activated in cancer. ERK regulates biological processes through phosphorylation of substrate proteins. However, in most cases the substrates that are phosphorylated for a given biological process are not known and the mechanism by which substrates achieve a biological outcome is unclear. The experimental animal model C. elegans has a single ERK ortholog, MPK-1, which functions in nine different processes that are necessary for germline development. The long-term objectives of this research program are to: 1) identify substrates of MPK-1 and to use germline development in this system to understand substrate function, regulation and regulatory interactions, and 2) determine whether the orthologs of C. elegans MPK-1 substrates are ERK substrates in mammalian systems, focusing on mouse oocyte maturation and Meiosis II (MII) arrest. A three-part functional genomics screen identified 25 MPK-1 substrates, which contain multiple ERK docking sites conserved in position with their mouse/ human orthologs, that function in one or more processes in C. elegans germline development. For a number of the substrates, phospho-specific antibodies were generated to verify MPK-1 dependent phosphorylation in vivo. We propose two lines of follow-up studies. The first is to use the C. elegans germline to understand temporal/spatial aspects of substrate phosphorylation, to understand how phosphorylation affects function and to investigate substrate mediated feedback regulation of MPK-1 activation. The second is to use the phospho-specific antibodies we have generated to test if the orthologs of MPK-1 substrates are ERK substrates in mammalian cell culture and in mouse cumulus enclosed oocytes. ERK functions in a number of processes within mouse oocyte meiotic maturation and MII arrest; the phospho-specific antibodies we have generated may be useful markers for oocyte development and may identify new substrates that act in maturation and MII arrest. Finally, we propose to extend our three-part functional genomic screen to identify new MPK-1 substrates using a different set of initial criteria. ERK is inappropriately activated in cancers where oncogenic mutations have occurred in the upstream signaling cascade members RAF, RAS and receptor tyrosine kinases (e.g. the EGF receptor). Since it is ultimately the substrates that are being inappropriately phosphorylated in these cancers that lead to ERK dependent phenotype, identifying the substrates and uncovering their function, regulation and regulatory consequences is essential part of understanding tumor biology and how it may be treated. PUBLIC HEALTH RELEVANCE: ERK MAP Kinase signaling is important in normal development and occurs inappropriately in many cancers (e.g. colorectal, melanoma, etc). It is the substrates that are phosphorylated by ERK that execute developmental processes and lead to uncontrolled growth and metastasis phenotypes in cancer. Identification of ERK substrates and characterization of their function is thus essential for understanding both normal development and cancer, where the substrates are potential biomarkers for outcome and therapeutic targets for cancer treatment. [unreadable] [unreadable] [unreadable] [unreadable] [unreadable]

Endometrial carinoma is the most common cancer of the female reproductive tract. Most endometrial cancers are found at an early stage and present with postmenopausal bleeding. These patients are initially treated with comprehensive surgical staging. This treatment is often diagnostic ofthe extent of disease and therapeutic. However, a key clinical problem in the management of patients with uterine cancers is how to best fre[unreadable]t~ab\r[unreadable]rhced'stagieclisease ahdlhe aggressive pathoTogic histotypes that account for signficant mortality. Patients with high stage or recurrent cancers have systemic disease requiring novel therapeutic interventions. Effective therapies are largely lacking. A better understanding ofthe cancer biology, such as signal transduction pathways, will lead to new treatment strategies that will improve the survival of these patients. Activation of the Mitogen Activating Pathway Kinase signaling pathway contributes substantially to endometrial tumorigenesis. Our group has identified thirty novel ERK substrates through a three-part functional genomic approach in the C. elegans model. The human orthologs of these proteins expressed in endometrial cancer cell lines are candidate ERK substrates. Thus far, of the candidates studied, we showed that GSK3n is important to cell growth in multiple endometrial cancer cell lines and has potential for therapeutic interventions.. In this proposal, we will continue to characterize novel ERK candidate substrates in endometrial cancer. In Aim 1, we will assess expression of candidate ERK1/2 substrates in the normal endometrium, primary endometrial cancers and endometrial cancer cell lines and determine if substrate phosphorylation is ERK-dependent. Then in aim 2, we will determine the relationship between ERK substrate phosphorylation status and upstream ERK signaling pathway activation in primary endometrial cancers and clinicopathologic significance of ERK substrate expression. Finally in aim 3, we will explore GSKSD inhibition as potential therapy for endometrial cancer and assess the role of inhibiting other ERK substrates plays in endometrial cancer cell lines. Together these studies should provide a better understanding of the role the ERK pathway plays in endometrial carcinogenesis and may lead to improved clinical biological therapies. RELEVANCE (See instructions): The work proposed will lead to both an improved understanding of endometrial cancer biology and new approaches to the detection, prevention and treatment of uterine cancers which will result in reduced cancer morbidity and mortality.

DESCRIPTION (provided by applicant): Tissues are formed and maintained by stem cells that produce both daughters that undergo self-renewing proliferation and daughters that differentiate. The mechanisms by which the choice between the self-renewal/ proliferative fate and the differentiated fate are made are not well understood in any system. However, disruption of the decision can cause stem cell loss, resulting tissue depletion, and lead to cancer. Our long-term goal is to understand how the proliferation vs. differentiation decision is made in the C. elegans germline. The C. elegans germline is the major model system for tissues where there are a larger number of stem cells that divide and differentiate through symmetric divisions, in contrast to the more widely studied systems with a small number of stem cells and differentiation through asymmetric division. The GLP-1 Notch signaling pathway induces the germ cell proliferative fate and represses three redundant pathways that promote the meiotic cell fate: the GLD-1 pathway, which acts in translational repression; the GLD-2 pathway, which acts in translational activation; and a third pathway whose existence has been revealed through genetic analysis but no gene products have been identified to date. Notch signaling in mammals is also important in stem cell self-renewal and oncogenic Notch activation can lead to cancer. Project goals address major unanswered questions in the field and include: (1) Determining whether the proliferative zone population is composed of only stem cells or both stem cells and proximal transit amplifying cells. (2) Identifying transcriptional targets of GLP-1 signaling for the proliferative fate and determining regulatory relationships with the three meiotic entry pathways. (3) Identifying the GLD-1 targets that are translationally repressed to promote meiotic entry.

DESCRIPTION (provided by applicant): WormBase Is the major publicly available database of information related to Caenorhabditis elegans, an important organism for basic biomedical research, and other nematodes of medical and agricultural importance. Although a crucial daily resource for members of the C. elegans research field, our users extend to the larger parasitology, biomedical, and bioinformatics research communities. WormBase acts as a central forum through which every research group can contribute to the global effort to comprehend nematode genomes. Most users access WormBase via the Internet (www.wormbase.orq). While some install the database locally. WormBase offers extensive coverage of C. elegans core genomic, genetic, anatomical and functional information, allowing the biomedical community to fully utilize the results of intensive molecular genetic analyses and functional genomic studies of this organism in the study of human disease. These data include all available nematode genomic data (such as genome sequence, transcripts and cis-regulatory sites prioritized by species), large-scale functional genomic datasets, the function and interactions of genes and gene products as they relate to development, physiology and behavior, and biological reagents and their source information. WormBase comprises a set of databases storing a wide range of biological information; a website that allows users to access stored information and precomputed analyses based on these data; and tools for programmatic access such as an application programming interface, a data mining platform, and bulk downloads. Curation activities include extraction and integration of information from the literature (assisted by the use of information retrieval tools), incorporation of large-scale datasets from a range of research projects, and gene model verification from experimental data. We will curate hundreds of nematode genome sequences, annotations and core genetic information as well as data on gene function, pathways and transcriptional regulatory networks for C. elegans and select other species. We will expand tools available for data mining, workflow management, visualization, and community annotation, and integrate, store and distribute data in a maintainable, interoperable and scalable system. The project team involves three sites: Caltech primarily curates functional information; EBI carries out sequence-based curation and builds databases for public release; and OICR develops and supports the web presence and visualization. The three sites work closely together and share tasks to ensure timely incorporation, storage and display of information. RELEVANCE Nematodes (roundworms) are major parasites of humans, livestock and crops, and understanding how to control them is a major world health and economic challenge. One species of nematode, C. elegans, is extensively used for basic biomedical research to elucidate how networks of genes affect cells, organs and a whole animal's development, physiology and behavior. WormBase collects, stores and displays information about the genomes and genes of C. elegans and other nematodes to facilitate research about this numerous and important group of animals.

DESCRIPTION (provided by applicant): ERK (extracellular signal regulated kinase) is the terminal kinase of the RAS-RAF-MEK-ERK pathway that controls numerous biological processes. Inappropriate ERK activation occurs in many cancers that contain oncogenic driver mutations in RAS, RAF or receptor tyrosine kinases such as EGFR and FGFR. ERK regulates biological processes through phosphorylation of substrate proteins. ERK substrates have been identified through individual gene approaches and more recently through discovery based proteomic approaches, although the functional role of many substrates is not known. We have taken a three part functional genomics approach that identified 30 substrates that function in seven different biological processes in C. elegans germline development: (1) bioinformatically identified candidate substrates that contain ERK docking sites conserved in position with the human ortholog; (2) RNAi tested function of the candidate substrates in ERK dependent biological processes using sensitized genetic backgrounds; (3) validated that the RNAi positive hit as a robust in vitro substrate of mammalian ERK2 and for a subset, demonstrated that ERK dependent phosphorylation occurs in vivo. Three conclusions came from our work: (A) Multiple ERK substrates control individual biological processes; (B) Substrates are molecularly diverse, affecting many parts of the cellular machinery, such as translation, RNA metabolism, cytoskeleton; (3) Substrates function cooperatively to promote a given process. Deregulated proliferation is a key aspect of cancer. The prevailing view from individual gene studies in the mammalian cell culture/cancer field is that RAS-ERK signaling promotes proliferation through transcription factor substrates. However the proteomic discovery and our functional genomic approach indicate that only ~12% of ERK substrates are associated with transcriptional control, the remaining affecting a wide range of cellular machinery. We propose that a number of ERK substrates that mediate proliferation remain to be discovered, particularly gene products that act in non- transcriptional cellular machinery, which can be identified in functional screens. Recently, a RAS-driven, ERK- dependent germline tumor model was reported for C. elegans, which provides an opportunity to identify ERK substrates that promote proliferation. We propose to apply our proven three part functional approach to identify C. elegans proteins, with human orthologs, that are ERK substrates that control proliferation in the RAS-drive, ERK-dependent tumor model. Discovery of ERK substrates with human orthologs will further our understanding of how RAS-ERK signaling promotes proliferation, provide a set of genes to be tested in mammalian cell culture models, may identify genes with cancer associated genomic alterations as ERK substrates, and may provide a framework/specific genes that can be used in cancer therapeutic approaches.

The proposed Dynamic Mining and Contextualization of the Scientific Literature (DMCSL) provides an open lane of communication between authors, science journals, readers, and databases. The outcome of this communication portal will be a database containing mineable metadata for researchers, reagent supply and biotech companies. Data will be available to companies through individualized subscription models. This pipeline identifies biological entities, e.g., gene, alleles, etc., and embeds hyperlinks from these entities to NHGRI-funded curated Model Organism Databases (MODs). DMCSL is an enhancement of a markup pipeline that has been in effect since 2009, and has linked biological entities in over 850 research articles in GENETICS and G3, published by the Genetics Society of America (GSA), to pages in MODs, WormBase, Flybase, and the Saccharomyces Genome Database. This proposal seeks funding to expand the scope of the GSA markup pipeline in all aspects: biological entities linked; authoritative databases linked to (Rat Genome Database; Mouse Genome Information; Zebrafish Model Organism Database; and the fission yeast genome database); and journals linked from. This expansion will also include collecting information on supplies and equipment described in Materials and Method sections of articles along with supplier information. The DMCSL will collect and store link information along with author and journal metadata and link access statistics. By doing so, the DMCSL will provide valuable metrics to all stakeholders, including biotech companies and life science vendors as well as a comprehensive and queryable view of biology not currently available. In Phase I, we will develop code that is flexible enough to scale the pipeline to link an article to more lexica and more databases within a single article and within a strict time limit of turnaround set by the publisher's production process. We will also be testing the software in linking publications of other journals and develop tools to query and data mine relationships identified through the data extraction process. We will develop basic API's to serve as a core API database resource; a linking API to store created links and monitor link activity, and use modern API management to develop a portal for key-based access to other API data. Proving stability and flexibility of the software based on current parameters, in Phase II we will work in collaboration with a wider range of stakeholders, more journals, more databases, including expanding to human biomedical databases, and more companies, to develop experience-based APIs for each stakeholder group. These APIs will be intuitively designed based on how each group interacts with the basic API developed in Phase I, and will be used to develop subscription-based access for commercial companies, access for academic stakeholders and collaborating journals will remain free.

Project Summary/Abstract The Streamlined capture and curation of unpublished data project will establish a new data capture and dissemination paradigm that automatically and simultaneously captures and ingests biomedical data into authoritative repositories and publishes them in an online, open access journal `Micropublication: biology'. This new platform will introduce a curation paradigm shift, allowing authors to directly submit the output of their research into pre-designed intelligent web forms. Upon submission, these forms will seamlessly integrate, atomize, and submit metadata into authoritative data repositories enhancing the efficiency and accuracy of curation. Simultaneously, the process will automatically generate a `publication-like' PDF file that will be publishable and citable according to findable, accessible, interoperable and reproducible (FAIR) data principles. We call these single result experiments, streamlined with no narrative ?micropublications?, ideal for among other things, results that often go unpublished. Authors will preserve provenance and establish credit for their research and the automated flow of data they submit will be made publicly accessible in established and authoritative data repositories such as the Model Organism Database (MOD) members of the Allied Genome Resources (AGR): FlyBase, Mouse Genome Database (MGI), Rat Genome Database (RGD), Saccharomyces Genome Database (SGD), WormBase, Zebrafish Model Organism Database (ZFIN), for further re-use. Through the aforementioned repositories, all submitted metadata will automatically be integrated with existing datasets that have been manually extracted from the literature for almost 2 decades. These data will be peer reviewed ensuring they are of high quality and that they meet community standards. Micropublications will be citable, discoverable, and will comply with the Minimum Information Standards for scientific data reporting. In addition, researchers will be able to share both positive and negative data with the scientific community, fulfilling funding agencies' requirements to share all data coming from publicly funded research. After establishing this data retrieval/publication pipeline with WormBase first, and AGR member databases, we will work to expand to non-member, but otherwise critical biomedical model organism databases, such as Xenbase (Xenopus laevis and tropicalis Database), DictyBase (Dictyostelium discoideum database), PomBase (Schizosaccharomyces pombe Database), among others.

Project Summary WormBase is the major publicly available database of information related to Caenorhabditis elegans, an important organism for basic biomedical research, and other nematodes of medical and agricultural signficance. Although a crucial daily resource for members of the C. elegans research field, our users extend to the larger parasitology, biomedical, and bioinformatics research communities. WormBase acts as a central forum through which every research group can contribute to the global effort to comprehend nematode genomes and biology. Most users access WormBase via the Internet (www.wormbase.org); some install the database locally. WormBase offers extensive coverage of C. elegans core genomic, genetic, anatomical and functional information, allowing the biomedical community to fully utilize the results of intensive molecular genetic analyses and functional genomic studies of this organism in the study of human disease. These data include all available nematode genomic data (such as genome sequence, transcripts and cis-regulatory sites prioritized by species), large-scale functional genomic datasets, the function and interactions of genes and gene products as they relate to development, physiology and behavior, and biological reagents and their source information. WormBase comprises a set of databases storing a wide range of biological information; a website that allows users to access stored information and precomputed analyses based on these data; and tools for programmatic access such as an application programming interface, a data mining platform, and bulk downloads. Curation activities include extraction and integration of information from the literature (assisted by the use of information retrieval tools), incorporation of large-scale datasets from a range of research projects, and gene model verification from experimental data. We will curate many nematode genome sequences, along with their annotations and core genetic information, as well as data on gene function, pathways and transcriptional regulatory networks for C. elegans and select other species. We will expand tools available for data mining, workflow management, visualization, and community annotation, and integrate, store and distribute data in a maintainable, interoperable and scalable system. The project team involves three sites: Caltech primarily curates functional information and develops ontologies; EBI carries out sequence-based curation and builds databases for public release; and OICR develops and supports the web presence and visualization. The three sites work closely together and share tasks to ensure timely incorporation, storage and display of information, as well as user outreach and education.

  Project Summary    This application proposes the Washington University in St. Louis School of Medicine (WUSM) Model Organism  Screening Core (wuMOSC) as a key asset for Phase II of the NIH Undiagnosed Diseases Network (UDN). The  wuMOSC  will  evaluate  the  pathogenicity  of  200  genetic  variants  per  year  identified  by  UDN  Clinical  Sites  in  otherwise  undiagnosed  participants  by  leveraging  the  optimal  combination  of  the  following  four  animal  model  organisms  and  human  cell-­based  Resource  Cores:  1)  C.  elegans,  2)  Drosophila,  3)  zebrafish,  and  4)  human  pluripotent  stem  cells  (hPSCs).  This  multi-­organism  approach  capitalizes  on  the  experimental  advantages  of  these  four  model  systems,  while  avoiding  the  limitations  of  individual  models.  Extending  the  established  advantages  of  the  Drosophila  and  zebrafish,  C.  elegans  allows  for  extremely  rapid  and  cost-­effective  variant  evaluation,  while  hPSCs  enable  assessment  of  genes  and  variants  that  are  not  conserved  in  animal  models.  An experienced Leadership Team has been assembled that harnesses the collaborative research environment  at WUSM, including the expertise of the McDonnell Genome Institute, and the superb WUSM clinical partners  that  constitute  the  proposed  UDN  Phase  II  WUSM  Sequencing  Center  and  Clinical  Site  applications,  respectively.  Using  proven,  cutting-­edge,  and  novel  bioinformatic  approaches,  combined  with  thoughtful  consideration of the advantages and limitations of each model organism, a careful assessment plan has been  defined for determining the putative pathogenicity of nominated variants and prioritizing them for experimental  evaluation  by  the  Resource  Cores.  Preliminary  data  demonstrate  that  all  four  Resource  Cores  are  using  efficient  and  advanced  genetic  targeting  techniques,  including  CRISPR/Cas9  to  knock-­in  the  human  variant  into  an  orthologous  gene,  knock-­down  and  loss-­of-­function  assays  where  appropriate,  and  overexpression  to  assess  rescue  of  loss-­of-­function  or  for  gain-­of-­function.  Phenotypic  analysis  of  the  genetic  models  will  be  guided  by  information  in  model  organism  databases  and  the  literature,  as  well  as  patient  symptoms.  This  information  will  then  be  applied  to  the  organism-­specific  and  extensive  phenotyping  pipelines.  The  UDN  Clinical  Sites,  Steering  Committee,  and  Coordinating  Committee  will  receive  frequent  communications  regarding  plans  and  results  of  the  wuMOSC,  through  the  activity  of  the  Administrative  Core,  which  will  also  disseminate acquired model organism expertise to the wider NIH and other research communities.  Therefore,  the multi-­model organism wuMOSC will have an exceptionally high impact on the diagnostic efforts of the UDN  by  bioinformatically  and  experimentally  evaluating  the  potential  of  disease-­causing  variants  in  the  context  of  disease-­specific phenotypes. 

Leadership/Implementation Project Project Summary This application proposes the Washington University in St. Louis School of Medicine (WUSM) Model Organism Screening Core (wuMOSC) as a key asset for Phase II of the NIH Undiagnosed Diseases Network (UDN). The wuMOSC will evaluate the pathogenicity of 200 genetic variants per year identified by UDN Clinical Sites in otherwise undiagnosed participants by leveraging the optimal combination of the following four model organism and cell-based Resource Cores: 1) C. elegans, 2) Drosophila, 3) zebrafish, and 4) human pluripotent stem cells (hPSCs). The combination of these model systems allows for extremely rapid and cost-effective variant evaluation in C. elegans, and evaluation in hPSCs of genes and variants that are not conserved in the animal model organisms, while maintaining the established advantages of the Drosophila and zebrafish models. An experienced Leadership Team has been assembled that harnesses the collaborative research environment at WUSM, including the expertise of the McDonnell Genome Institute, and the superb WUSM clinical partners that constitute the proposed UDN Phase II WUSM Sequencing Center and Clinical Site applications, respectively. Using proven, cutting-edge, and novel bioinformatic approaches, combined with thoughtful consideration of the advantages and limitations of each model organism, a careful assessment plan has been defined for determining the putative pathogenicity of nominated variants and prioritizing them for further evaluation by the Resource Cores. The leaders of the four Research Cores have significant expertise in the relevant model system, and are currently employing the proposed advanced genetic approaches (CRISPR/Cas9 knock-in, tissue-specific RNAi and overexpression, and testing variant mRNA for null mutant rescue) and extensive phenotypic analysis to assess human gene variants for effect on gene product function. The UDN Clinical Sites, Steering Committee, and Coordinating Committee will receive frequent communications regarding plans and results of the wuMOSC, through the activity of the Administrative Core, which will also disseminate acquired model organism expertise to the wider NIH and other research communities. Therefore, the wuMOSC will have an exceptionally high impact on the diagnostic efforts of the UDN by bioinformatically and experimentally screening potential disease-causing variants in the context of disease-specific phenotypes.

The Washington University (WU) Model Organism Screening Center (wuMOSC) will utilize four model organisms, C. elegans, Drosophila, zebrafish and hPSC, for functional analysis of gene-variants nominated by Undiagnosed Disease Network (UDN). C. elegans is a major model organism for studies of animal cell and developmental biology, excelling at gene function discovery and elaboration of pathways in which gene products act. A number of features make C. elegans appropriate for being the first line organism for experimental assessment of UDN variant on gene product function. These include short generation time (4 days), small size, inexpensive maintenance, self-fertile hermaphroditism, and optical transparency that permits detailed phenotypic analysis at all stages of the life cycle. About 60% of human genes have an ortholog in the C. elegans genome, indicating that a substantial portion of potential disease genes can be experimentally examined in the worm. C. elegans research has advanced our understanding of disease. For example, published work has demonstrated that variant knock-in can recapitulate the effect on gene product function for known diseases, provide support for phenotypic expansion and provide support for molecular diagnosis of a UDP gene. In a project paralleling the activities of Phase I UDN MOSC, we have been collaborating with the WU Pediatric Genetics Clinic to examine candidate gene-variants of uncertain significance found in patients that did not receive a molecular diagnosis, by CRISPR/Cas9 variant knock-in into the C. elegans ortholog and assessing if there is a change in function. This work indicated that ~1/3 of patient variants can be assessed by knock-in with the worm, given conservation of both the gene and variant residues. Importantly, CRISPR/Cas9 mediated homology directed knock-in of variants occurs at very high frequency, allowing us to obtain variant knock-in strains, out-crossed twice, in ~3 weeks. The wuMOSC Leadership Project, working in conjunction with the C. elegans Resource Core, will assign ~60 UDN gene-variants for function analysis in the worm. The variants will be knocked into the orthologous worm gene. To assess function, a prioritized phenotyping pipeline will be employed that includes 7 different phenotyping platforms, from simple morphological analysis, to high-throughput assays for viability, growth, reproduction, to assessment of movement/behavior and custom assays that are derived from published phenotypes for the gene of interest. The pipeline allows focusing on known phenotypes or broad searches for unknown phenotypes, increasing the likelihood of detecting a phenotype. High-throughput phenotypic assays are important because of the large number of genes and genotypes that will be analyzed. Results from phenotypic analysis will inform on the functional effect of the variant, which will be communicated to the UDN, providing information that can contribute to a diagnosis.

Abstract A key point in germ cell development is the switch from stem/progenitor cells to meiosis and gametogenesis. Disruption of this developmental switch can result in infertility and in some cases germline tumors. The C. elegans adult hermaphrodite is an important model for understanding control of the switch from germline stem cell fate to meiotic development/gametogenesis, where a network controlling the process is emerging. Niche dependent GLP-1 Notch signaling promotes the stem cell fate through repressing three redundant posttranscriptional pathways that promote meiotic entry: the GLD-1 pathway (which represses expression of mitotic cycling genes), the GLD-2 pathway (which promotes expression of meiotic genes), and the SCFPROM-1 pathway that both degrades mitotic cell cycle proteins at meiotic entry and initiates homologous chromosome pairing. Current studies indicate that while transcriptional programs set the stage, it is largely posttranscriptional regulation that executes meiotic entry in animals. At a cellular level, we have shown that in C. elegans the stem cell population is large and germ cells enter meiosis directly, without intervening transit- amplifying divisions. The absence of transit-amplifying divisions simplifies the analysis allowing straightforward assays to identify genes involved in repressing meiosis in stem cells and repressing mitotic cell cycling at meiotic entry and is the primary reason why C. elegans is a major animal model for studying this important developmental switch. This proposal addresses three major gaps in knowledge and a major technical challenge in molecular/ biochemical mechanistic studies of the stem cell/progenitor switch to meiotic development in C. elegans. First, it is not known how SCFPROM-1 is repressed in stem/progenitor cells. Second, the mRNA targets of the GLD-1 translational repressor and the GLD-2 translational activator, which repress mitotic cycling and promote meiotic gene product accumulation, are largely unidentified. Third, mechanisms by which GLP-1 signaling is restricted to the stem cell niche region are not fully known, and the mechanism by which the mett-10 m6A methyltransferase inhibits GLP-1 signaling is undescribed. Molecular/biochemical studies of the switch from stem/progenitor cells to meiotic entry are limited by the C. elegans germline containing all stages, present in an assembly-line order from stem cells to mature gametes, with any given stage a small proportion. We will develop a genetic system for the synchronous switch from stem cells to meiotic entry, in a sufficiently large population of germ cells and animals to allow molecular/biochemical studies.