Peter S. White, Ph. D. - US grants

Loblolly pine (Pinus taeda) dominates the early successional forests of the North Carolina Piedmont. Scarcity of resources, especially light, causes the stands of pine to undergo thinning: as the trees grow larger, competition for light escalates and the shorter, shaded individuals suffer high mortality. Several investigators have found that in some forest tree species, genetic heterozygosity is low in young stands and high in older stands. This trend is the likely result of the culling of the more homozygous individuals when the stands undergo thinning. Research is proposed to determine whether those individuals with high heterozygosity are less likely to die, and whether the average heterozygosity of the survivors in a stand reflects the intensity of competition for resources as determined by initial stand density. This research proposes to explore the natural processes which influence genetic structure in forest stands. Natural forest stands, as opposed to pine plantations, may maintain higher genetic diversity as a likely benefit of heterozygous individuals through thinning of dense stands. The genetic effects of natural stand thinning could have important implications for forest management efforts aimed at maximizing tree vigor and forest productivity.

9707551 Peet Much of the current uncertainty regarding the nature and mechanisms of forest succession is a consequence of the paucity of long-term data sets, particularly those dealing with patterns of establishment, growth, and mortality of individual plants. The forests of the North Carolina Piedmont have long been viewed as a model system for the study of secondary succession, in part because of the availability of long-term records of forest development. Among the key issues that remain to be resolved are the processes that influence community reorganization during the transition from even-aged to all-aged stands and the role of large, infrequent disturbances. This project will continue measurements of a rich assemblage of long-term research plots in and near the Duke Forest and thereby enhance the value of this site as a model system for the study of succession. In September 1996, many of the long-term plots were impacted to various degrees by Hurricane Fran which provides a new direction and opportunity for this project. Major disturbances like hurricanes are known to play an important role in forest dynamics, but rarely do such events occur on sites with a sufficient long-term history of research to allow assessment of the changes in ecological processes induced by the disturbance event. A second focus of tis study will be the documentation and archiving of the Duke Forest data, including standard metadata, for distribution to current and future researchers. Ultimately, these data will be freely accessible to investigators via standard network protocols.

The identification of disease genes for complex disorders has been greatly facilitated by recent advances in structural genomics. While several unidimensional genetic, physical and transcript maps of the human genome have been instrumental in identifying single-locus disease loci, these maps lack the integration and resolution required for precise localization of transcripts involved in complex genetic diseases. We have developed a method for viewing whole chromosomes which unites mapping data from multiple experimental sources onto a single scale, thus providing higher resolution, greater statistical confidence of marker placement, and superior integration than current maps. This procedure (CompView) provides a comprehensive and seamless representation of human chromosomes, simultaneously presenting clinical, biological, and structural perspectives. CompView has been successfully implemented for human chromosome 1 to localize 5,000 unique markers and 8,000 large-insert clones with a marker density of 50 kb and a resolution of 900 kb. Here, we propose to further refine this procedure and extend it to include the entire human genome. First, we will construct 1 Mb resolution framework maps of each human chromosome with an iterative process to maximize map resolution. Second, we will integrate existing genetic, cytogenetic, radiation hybrid, expressed sequence tag, physical mapping, and sequence data with our established frameworks. Furthermore, we will continue to streamline and automate the map construction process, will explore methods for including regional and chromosome-specific mapping information, and will seek to integrate additional mapping, sequence, and functional genomic data as it becomes available. Third, we will continually assess our generated framework and integrated maps, as well as the underlying genomic data, for marker placement inconsistencies. Discrepantly mapped genomic elements will be identified and either removed or re- localized, and marker positions will be refined by comparison with identified order in large genomic sequence tracts. Fourth, we will expand an existing Internet-based user interface that provides text-based and graphical viewing options for map presentation. The Internet site will be an exhaustive and immediate data portal for all available genomic information for a specific region, marker, or transcript. This project will quickly refine localizations of over 46,000 human transcripts, creating a resource for the entire biomedical community. Completion of this project will facilitate the identification of additional loci involved in mental illnesses, especially in defining chromosomal regions and candidate genes for quantitative trait loci contributing to such complex behavioral afflictions as schizophrenia, bipolar disorder, Alzheimer's disease, alcoholism and clinical depression.

Our multidisciplinary team of clinicians and researchers seeks novel patient-individualized approaches for understanding and managing pediatric acquired aplastic anemia (aAA), a rare but devastating condition characterized by bone marrow hematopoietic stem cell (HSC) hypoplasia with life threatening bleeding, anemia and infections. Pediatric aAA is believed to occur via immune cell attack of HSCs, but little more is known about the pathogenesis and current treatments are not mechanism-based. Some patients with aAA develop clonal hematopoiesis, which is typically viewed pessimistically as a sign of impending myelodysplasia or leukemia. However, this may not always be the case, as our preliminary studies have identified numerous aAA patients with clonal hematopoiesis who have been in healthy remission for years. Moreover, many of these patients harbor unique mutations within their dominant hematopoietic clones. Thus, we hypothesize that clonal hematopoeisis in aAA results from mutational events that impart a growth or survival advantage to HSCs or early progenitors, particularly in the face of disease-associated insults. We will use modern genomic approaches to define the scope of these mutations in a large cohort of aAA patients (Aim 1), follow the clinical course and genetic evolution of the patients longitudinally (Aim 2). Several unique aspects of our study enhance its likelihood of success: First, we are a team of investigators with broad, synergistic expertise in the clinical management of aAA, bioinformatics and genomics/genetics. The ability to follow all of the patients longitudinally in a comprehensive pediatric-adult bone marrow failure clinic at The Children's Hospital of Philadelphia and The Hospital of the University of Pennsylvania. Finally, our study will utilize a large clinically well-annotated tissue collection obtained serially from over 100 aAA patients over 13 years, consisting of DNA and cryopreserved skin, blood and bone marrow cells. We will continue to follow these patients clinically and procure additional samples throughout the study. If successful, our work will identify sets of genes and gene mutations that will sub-classify aAA molecularly to predict prognosis more accurately and to identify more effective, mechanism-based patient-specific therapies.

? DESCRIPTION (provided by applicant): Congenital heart defects occur in approximately 40,000 infants in the US each year and are a major cause of infant death. The Bench to Bassinet Program (B2B) was launched by the National Heart, Lung, and Blood Institute (NHLBI) to accelerate pediatric cardiovascular translational research from discovery to early translational testing to clinical testing. Components of the B2B program include the Cardiovascular Development Consortium (CvDC), Pediatric Cardiac Genomics Consortium (PCGC). The objectives of the CvDC are to generate and disseminate comprehensive data about molecular networks and pathways that regulate cardiovascular development. Objectives of the PCGC are to identify genetic causes of human congenital heart disease and to relate genetic variants present in the congenital heart disease patient population to clinical outcomes. The consortia interact with each other, and with the NHLBI Pediatric Heart Network (PHN) to efficiently translate results from basic science to clinical research, and to provide clinical input on pressin needs for basic research. The Administrative Coordinating Center (ACC) provides the infrastructure to enhance collaborations among the consortia and to identify and facilitate the translational research process for the most important pediatric cardiovascular clinical care problems. The ACC will drive standards that are required for data integration and sharing, leading to reproducibility of results. Our proposed ACC to support the CvDC and PCGC is a unique, integrated combination of world-leading pediatric cardiovascular and neurocognitive clinical/translational research expertise, advanced infrastructure, outstanding institutional support, and state-of-the-art technology. We believe these strengths to be critical for an ACC to successfully partner with the B2B program and NHLBI in leading the coordination of knowledge and data for this important pediatric cardiovascular research effort. Synopsis Research for patients with congenital heart disease requires a cooperative and coordinated effort among research programs to efficiently translate results from basic science to clinical research, and to provide clinical input on pressing needs for basic research. Our proposed ACC to support the CvDC and PCGC is a unique, integrated combination of world-leading pediatric cardiovascular and neurocognitive clinical/translational research expertise, advanced infrastructure, outstanding institutional support, and state-of-the-art technology.

Project Summary/Abstract Rare diseases (RD) and disorders collectively affect about 25 million Americans. RD research and care face common challenges, including: 1) insufficient knowledge about the etiology, pathophysiology, natural history and epidemiology of the diseases; 2) inadequate or non- uniform case definition and disease classification systems that make diagnosis and epidemiologic assessment difficult; 3) insufficient understanding of the determinants of multiple phenotypes and the relationships between genetic variance and phenotypic manifestations; 4) rarity and geographic dispersion of cases that hampers both access to qualified care and participation in research; 5) a dearth of clinically proven, safe and effective treatments; and 6) inadequate private investment into RD research and treatment. In the U.S., the Rare Diseases Act of 2002 authorizes the Office of Rare Disease Research to recommend a research agenda and promote coordination and cooperation among research programs. The Rare Diseases Clinical Research Consortia (RDCRC) that comprise the Rare Diseases Clinical Research Network (RDCRN) advance the diagnosis, management, and treatment of RDs to enhance clinical trial readiness. The RDCRN Data Management and Coordinating Center (DMCC) must provide state-of-the-art informatics, statistical and epidemiological expertise in clinical research study design and data management technology and processes, in order to guarantee the production of evidence that can support the progression of clinical and translational research (CTR) from Phase I through Phase III trials to adoption within standard clinical practice. To achieve the goal of enhancing clinical trial readiness throughout the RDCRN, we will establish the DMCC at Cincinnati Children?s and the University of Cincinnati with the following Specific Aims: 1): To advance the methods and the practice of RD CTR; 2) To develop and maintain a leading-edge, shared knowledge base for RD CTR; and 3) To establish the RDCRN as a globally connected resource for improving RD CTR across the entire RD ecosystem. We expect to accomplish these Aims by promoting collaboration and trial readiness, engaging patients and families, and creating an ?Esprit de Corps? for the RDCRN, through the adoption of Learning System principles. Our proposed DMCC brings a unique combination of world-class expertise, outstanding infrastructure, state-of-the-art technology and enthusiastic institutional support. This winning combination will accelerate scientific discovery and understanding across the network, which will bring new treatment options to trial, ultimately translating into improved health and wellness for RD patients and their families worldwide.

PROJECT SUMMARY Approximately 795,000 people have a stroke in the U.S. every year, and about 6.3 million people died from stroke worldwide in 2015. There are many different pathophysiological processes that can result in stroke, and thus, stroke does not demonstrate a single pathology. The two main classifications of stroke are acute ischemic stroke (AIS), caused by a blockage of blood flow to the brain, and hemorrhagic stroke, the most common type of which is intracerebral hemorrhage (ICH), caused by bleeding into the brain. The extensive pathophysiological response during a stroke is complex and involves multiple mechanisms, including throm- bosis, inflammatory and excitotoxicity responses, and apoptosis, all of which contribute to neuronal injury, cell death, and the breakdown of the blood brain barrier (BBB). High-density lipoproteins (HDL) play a critical role in the prevention of CVD and have been found to form distinct stable subspecies, each with their own unique complement of proteins and lipids, some of which are implicated in disease processes associated with di- verse types of diseases. Several clinical studies have shown an inverse relationship between HDL-C (choles- terol) and stroke risk. Our previous research discovered that the HDL-associated proteins apolipoprotein A-I and paraoxonase-1 were less abundant in AIS compared with healthy subjects. To further explore these find- ings, the objective of this application is to identify HDL subspecies that are related to stroke and to eluci- date their mechanistic connection with stroke. We hypothesize that by analyzing the HDL proteome in stroke patients compared with non-stroke subjects, we can identify specific HDL subspecies that are involved in stroke pathophysiology, specifically those subspecies that are likely to affect stroke pathogenesis through one of HDL's many known functions, in particular, its anti-thrombotic properties. We will pursue the following spe- cific aims: (1) Proteomic profiling of HDL subfractions from stroke and non-stroke subjects (Years 1-3). (2) Computational identification and prioritization of stroke-related HDL subspecies in plasma (Years 2-4). (3) Experimental validation and mechanistic evaluation of stroke-related HDL subspecies (Years 3-5). This proposal is a renewal of the PI's first R01 grant (R01-HL111829, 08/01/2012-06/30/2018). It is a nat- ural extension of our prolific research on HDL subspecies and their role in healthy subjects to now focus on stroke. The proposal builds on the solid clinical evidence linking HDL and stroke, yet is highly innovative in that it will be among the first to definitively associate HDL subspeciation with stroke. As such, it will fill a major gap in our understanding of the compositional and functional heterogeneity of HDL particles and defining their association with stroke. Our research will have a significant impact because it will facilitate our molecular understanding of HDL functions by revealing the mechanisms by which HDL subspecies affect stroke pathol- ogy. Further investigation of these HDL subspecies in the long-term has the potential to substantially improve the current diagnostic and treatment paradigm for stroke and optimize outcomes for this devastating disease.

PROJECT SUMMARY The LungMAP 2 initiative will create detailed molecular maps of the neonatal, pediatric and early adult human lung to enable improved understanding of functionally and anatomically defined cell types. The Data Coordination Center (DCC) will serve as the nexus of LungMAP 2's collective knowledge and activities. The DCC is responsible for data collation, re-analysis, and integration; secondary annotation tracking; developing tools to facilitate collection, sharing and data dissemination; operating a web resource for data, expertise, and collaboration; and coordinating activities across the Research Centers (RCs) and Human Tissue Core. The DCC will also facilitate literacy for investigator use of developed tools and best practices for analysis, data provenance and metadata annotation, and engage the larger research community. To host the DCC, we have assembled a multidisciplinary team with data network leadership, along with leaders in single-cell genomics, image analysis, functional inference, and data re-utilization. The DCC leverages unique expertise at CCHMC, UCSC, and the Broad Institute to interoperate pulmonary-oriented single-cell and high-resolution imaging data with other atlas programs. We also include world-renowned pulmonary researchers into our leadership team to ensure the data and knowledge we provide to the research community has the greatest scientific impact. Collectively, we propose to accelerate the LungMAP scientific agenda by coordinating efforts across funded Centers, the NIH, and the pulmonary research community; cross-validate, annotate, deposit and link Consortium datasets and metadata that encompass molecular -omics, imaging, and associated structural models; and enable sharing of data, results, and models within LungMAP and the research community. The datasets and results derived from the RCs are expected to yield significant new insights into lung maturation, intra-donor variation and disease pathogenesis. To ensure the underlying data produced by the RCs is findable, accessible, interoperable and re-usable (FAIR), the DCC will work closely with the RCs to establish and share best practices, coordinate metadata annotation, ensure studies are sufficiently powered, assist with the deposition of harmonized data of high integrity to secure repositories, and provide data access and standardized analysis workflows. Through the continued development of structured ontologies and metadata frameworks, RC-derived datasets will be annotated and harmonized using emerging best practices. The DCC will support the ingestion and validation of data and analysis from new technologies as they emerge. We will support the generation of centralized, cloud-enabled data processing workflows that are compatible with external initiatives such as HubMAP, BRAIN, and the HCA. We expect that providing these functions in a web-enabled LungMAP Commons will promote interaction across many stakeholders. This will position the LungMAP DCC to become a hub for data sharing, data integration, collaboration and hypothesis generation for investigators studying lung development and disease.