University Of Calif-Lawrenc Berkeley Lab

NIH Research Projects · FY 2025 · 2009-09

PROJECT SUMMARY/ABSTRACT This project is aimed at understanding the processes that drive decline in cognitive function with aging. Over the past decade it has become increasingly clear that many normal individuals often harbor the pathology that is associated with Alzheimer’s disease (AD): β-amyloid (Aβ) plaques and pathological accumulation of the microtubule associated protein tau. With the ability to detect and track these pathologies during life using multiple techniques including positron emission tomography (PET), we have learned that Aβ and tau pathology are associated with, and can predict decline in cognition, particularly episodic memory (EM), in otherwise cognitively normal people. Nevertheless, there is considerable variability associated with how individuals respond to AD pathology. Some show resilience: that is, they do not display impairment in EM despite evidence of pathology, while others may demonstrate resistance: they do not show evidence of pathology when existing group level data predicts its occurrence. The next phase of this project is oriented towards understanding how some people show successful aging outcomes despite the presence of AD pathology or show lower levels of pathology then expected. We will begin by defining two groups of successful agers from the Berkeley Aging Cohort Study (BACS) who have 3 or more longitudinal visits. The first definition makes use of a widely applied approach to select individuals performing at high levels in cross sectional cognitive measures. We refer to these as exceptional agers (EA) and will use a novel method deploying machine learning to predict “cognitive age” from a battery of neuropsychological tests. Those who fall in the “youngest” 20 percent of the cognitive age gap (CAG – difference between actual and predicted age) are defined as EA. Second, we will use a novel approach to define successful agers as those who show maintenance of EM performance over time, that is a slope of 0 or above on an EM composite measured at 3 or more timepoints. All of these individuals will receive longitudinal neuropsychological testing and PET scanning for AD pathology: Aβ PET with [11C]PIB and tau PET with [18F]Flortaucipir. At the first visit in this grant phase, participants will have an added PET scan to measure synaptic density with the ligand [18F]SynVesT1 that binds to the synaptic vesicle 2A protein. Based on extensive preliminary data, we predict that several different mechanisms underlie successful aging outcomes despite AD pathology: (1) Thicker mid-cingulate cortex will confer resilience to the effects of tau on EM decline (2) Successful agers will show less tau pathology and slower rates of Aβ and tau deposition because they are in earlier stages of Aβ deposition and (3) synaptic density in successful agers will be greater in specific brain regions including prefrontal cortex and mid-cingulate cortex and this will also confer resilience to AD pathology.

NIH Research Projects · FY 2025 · 2006-09

PROJECT SUMMARY Hundreds of thousands of distant-acting enhancers control the function of the human genome by orchestrating the transcription of genes during pre- and postnatal development and in normal and disease states of cells and tissues. They display remarkable cell type specificity and dynamic spatial and temporal activity patterns. While there is now abundant indirect evidence that sequence changes in enhancers are likely to impact substantially on human phenotypic variation and many disease processes, our understanding of how biological function is encoded within enhancer sequences remains incomplete. This represents a major challenge for the interpretation of variation in enhancer sequences observed by whole-genome sequencing (WGS) in patients and for linking sequence variants within enhancers to diseases and other phenotypes. Over the past 16 years, the research program supported by this R01 has provided major insights into enhancer biology and groundbreaking tools for enhancer discovery and characterization. This included the first demonstration of ChIP-seq from mammalian tissues for enhancer discovery, and a constantly evolving suite of mouse engineering methods for studying enhancers in vivo. This program has also produced the largest cohesive collection of human and mouse in vivo-characterized enhancers available to date and provides the VISTA Enhancer Browser as a major community resource. In the next phase of this research program, we propose to leverage the unique capabilities previously developed under this program to further advance our understanding of general enhancer biology, to complement the work of the recently established NHGRI Impact of Genomic Variation on Function (IGVF) consortium with critically needed in vivo assessments of enhancer variants, and to provide enhancer resources for the extended community. Our specific aims include: (1) We will explore the inner anatomy of enhancer sequences through large-scale mutagenesis coupled to in vivo mouse assays. We will also delete large non- coding genome intervals (gene deserts) from the mouse genome to determine the broad functional significance of non-coding DNA beyond individual enhancer elements. (2) Working as Affiliates with the IGVF Consortium, we will perform large-scale in vivo exploration of human variants with predicted impact on enhancer function to assess human variation/mutation through our unique mouse engineering capabilities. This will include careful validation and calibration of massively parallel reporter assays (MPRAs) and CRISPR screens through comparison with in vivo mouse reporter assays. (3) We will continue to provide access to in vivo mouse assays for the community and make our results available through the VISTA Enhancer Browser. In combination, in the next phase of this program we expect to deliver impactful insights into the biology of enhancers as a major category of non-coding genome function, apply innovative tools to demonstrate the in vivo impact of variants identified by the IGVF consortium, and continue to make unique enhancer analysis tools and resources available to the broader community.

NIH Research Projects · FY 2025 · 2001-09

SUMMARY DNA repair maintains genome stability to prevent cancer and provides resistance to cancer treatments; yet, DNA repair defects lead to cancer-causing mutations and are an Achilles heel for cancer-targeted treatments. Structural Cell Biology of DNA Repair Machines 5 (SBDR-5) coordinates leaders in DNA repair (DR) to work together synergistically for comprehensive mechanistic and structural knowledge of DR processes. Four interacting Projects (P1-4) target DR pathways implicated in cancer etiology, treatment, and resistance: P1 investigates repair of base lesions from chemotherapy including a paradigm-shifting model for RNA damage responses to alkylating agents. P2 defines inter-locking pathways for repair of dsDNA breaks (DSBs), a result of radiation therapy as well as replication encounters with DNA lesions. P3 examines PARylation-mediated phase condensates and their impacts on DR for PARP inhibitor therapies. P4 determines mechanisms in replication fork stress responses, key consequences of many cancer treatments. Our highest priorities are to solve actionable structures in each Project and apply our teamwork to biochemically and biologically test molecular insights and hypotheses based on our structures. Two experimental Cores will enable efficient preparation of DR assemblies and determination of their structures. Removing bottlenecks within individual laboratories and promoting collaborative efforts, SBDR Projects and Cores together enable a comprehensive cross-pathway knowledge of dynamic multi-functional DR machines – knowledge best achieved through multi-disciplinary approaches and concerted efforts by multiple groups. Our four Program aims are: 1) Determine actionable and biologically-validated structures of DR complexes, interfaces, and conformations. 2) Dissect multi-functionality of DR machineries tested by structure-based design of separation-of-function mutations and chemical inhibitors to inform on predicted therapeutic sensitivity and development of resistance. 3) Define DR pathway interactions and crosstalk with replication dynamics to delineate DR pathway outcomes. 4) Discover synthetic lethality from mutations or chemical agents that target specific DR activities and which become essential only in conjunction with another DR defect to promote successful therapeutic interventions. SBDR will provide lasting structure-based knowledge for interpretation of mutations from The Cancer Genome Atlas and of mechanisms that inform system level knockout and knockdown correlations. Through concerted efforts, SBDR-5 will establish biologically-validated structures and synthetic lethality relationships with durable biological and medical utility. We will share constructs, mutants, inhibitors, data, and technologies to enhance synergy, reproducibility, and efficiency. Our target structures and mechanisms are both challenging and timely: the expected results will have indelible impacts on ongoing NIH research in other labs, on assessment of cancer genome data, and on knowledge for treatment strategies in ongoing clinical and preclinical trials of DR inhibitors.