ADRC Research
The Stanford Alzheimer’s Disease Research Center (ADRC) supports internal research in the form of developmental projects and Research Education Component (REC) fellowships. Developmental projects are usually conducted over a two year period and are funded for up to $250,000 each. The ADRC has selected four projects (two in 2020 and two in 2021), and we anticipate new projects in 2022 and 2023. Developmental project grants are intended for junior faculty level investigators and for more senior investigators whose research lies in other areas and who now want to work in the field of Alzheimer disease and related disorders.
The Stanford ADRC contributes de-identified data and biological resources to registries and repositories supported by the National Institute on Aging. It supports other research at Stanford University and at other institutions. Center support can include de-identified data (clinical, neuropsychological, structural and molecular brain imaging, genetic, ‘omics, microbiome, and neuropathological), fluid biospecimens obtained from ADRC volunteers (plasma, CSF), fibroblast cell lines, autopsy tissues, biostatistical consultation, and research guidance.
The Stanford ADRC supports research training and education in a variety of ways. The REC fellowship program is described more fully below. This program provides integrated clinical and basic science training opportunities and mentored research experiences. It is designed to prepare the next generation of researchers for careers in brain aging and in Alzheimer’s disease and related disorders.
Tabs below provide additional information on developmental projects, REC fellowship projects, ADRC publications, and application materials for both developmental projects and REC fellowships. Titles of internal research supported by the Stanford ADRC during the 2015–2019 funding period are also shown.
Developmental research project (2021) 2.1
Principal investigator: Andrew Gentles, PhD, Assistant Professor, Depts of Medicine (Biomedical Informatics Research) and Biomedical Data Sciences
Title: Cell type specific transcriptional changes in neurodegenerative disease
Project description: Understanding changes in gene expression in specific cell types between normal and diseased brain is crucial for understanding disease mechanisms and identifying novel therapeutic targets. Recovering cell type specific gene expression from tissues is also a major first step towards reconstructing cell specific transcriptional networks, and inferring cross-talk between cell types in disease states. Single cell RNA-seq is widely used, but it is expensive and requires extensive sample processing, which can distort cellular content in tissues and perturb their functional states. Bulk RNA-seq can be applied cost-effectively to large cohorts of clinically annotated patient samples, including archival materials, but it conceals cell type specific changes in gene expression between normal and diseased brain tissue. Computational deconvolution methods applied to gene expression data from bulk tissues can estimate the proportion of different cell types in the mixture and recover cell type specific gene expression data. This approach opens the possibility of identifying cell type specific differences in gene expression between normal and disease tissues without dissociation and single cell processing. We propose to optimize such approaches for the cell types present in brain and validate them for human and mouse in silico. We will deconvolute bulk RNA-seq from human samples with known “ground truth” determined by CODEX (CODetection by indEXing) proteomic imaging. We will then apply this framework to large clinically-annotated data cohorts acquired from normal brain and neurodegenerative disease. We will focus on Alzheimer disease and vascular dementia to identify specific hypotheses that will be experimentally testable by collaborators at the Stanford ADRC.
Developmental research project (2021) 2.2
Principal investigator: Harini Iyer, PhD, Postdoctoral scholar, Developmental Biology
Title: Lysosomal signaling in microglia and Alzheimer’s disease
Project description: Genome-wide association studies of Alzheimer’s disease (AD) patient mutations implicate immune pathways in disease onset or progression. Microglia, the primary immune cells residing in the brain, ensure nervous system well-being and function by eliminating dying cells, pruning neural connections, and orchestrating appropriate immune responses. Two key microglial processes – lysosomal activity and inflammatory response – are aberrantly involved in neurodegenerative diseases, but it is not known how these microglial activities become dysfunctional in AD. My preliminary studies demonstrate the importance of two key lysosomal transcription factors, Tfeb and Tfe3 (Tfeb/3), in the function and maintenance of microglia in zebrafish. Although zebrafish cannot be directly used to study AD pathology, their advantages include amenability to live imaging, feasibility of large-scale mutagenesis screens, and optical transparency of embryos. Furthermore, culturing microglia in vitro results in rapid loss of microglial identity. Human TFEB/3 may regulate immune genes in macrophages (progenitors of microglia), and TFEB/3 may be dysregulated in AD. However, the extent to which disruption of TFEB/3 activity in microglia contributes to the pathology in AD is not known.
I have defined a lysosomal regulatory circuit acting upstream of Tfeb/3 in microglia, and in the next phase of my training, I will identify downstream targets of Tfeb/3 using RNAseq in loss and gain of function mutants. I will compare differentially expressed genes to publicly available AD databases. I will use CRISPR mutagenesis to show how Tfeb/3 activity is disrupted in AD to uncover the functions of Tfeb/3 targets. These experiments will advance my training in CRISPR/CRISPRa screens, analysis of AD patient databases, methods to identify and image microglia in vivo, and assays of microglial function (e.g., engulfment and elimination of neuronal debris). Disruption of microglia activity in AD is well appreciated, but a large-scale functional genomic screen of genes associated with AD mutations has not yet been performed.
As an independent researcher, I will capitalize on my training in microglial imaging and lysosomal biology to study genes associated with patient mutations in AD. I will identify zebrafish homologs of genes mutated in AD, prioritize them based on microglial expression or lysosomal function, and perform CRISPR knockout or CRISPRa gene activation, followed by characterization of microglial responses. My proposed research renders microglial biology accessible to live imaging and functional characterization in vivo, and it bridges the gap between genomic resources available for AD and the cellular and molecular mechanisms underlying the pathology of this devastating disease.
Developmental research project (2020) 1.1
Principal investigator: Monther Abu-Remaileh, PhD
Title: Molecular basis of lysosomal dysfunction in neurodegeneration
Project description: Lysosomes are small compartments within nerve cells where macromolecules and damaged organelles are degraded and cleared. Lysosomes serve as major regulators of cell signaling, metabolism and longevity; and lysosomal dysfunction is implicated in causing Alzheimer’s disease and Parkinson’s disease. There is an urgent need to understand the molecular and biochemical basis of lysosomal dysfunction in age-associated neurodegenerative diseases to determine its role in disease pathology. This is a challenging task, because there are few tools to probe the protein, small molecule, and RNA contents of lysosomes. To overcome this hurdle, we recently developed a method to immunopurify lysosomes from cells and tissues, a method we call LysoIP. Purified lysosomes are suitable for small molecule profiling using liquid chromatography and mass spectrometry. In this proposal, we hypothesize that lysosomal dysfunction drives age-associated neurodegeneration. By profiling lysosomes from cells derived from skin biopsies of patients with Alzheimer’s disease and Parkinson’s disease, we will determine the exact biochemical basis of lysosomal dysfunction in these two disorders. We have three aims:
Aim 1: Using our innovative technology, we will generate LysoTag fibroblasts obtained from Alzheimer’s disease and Parkinson’s disease patients enrolled in the Stanford Alzheimer's Disease Research Center.
Aim 2: We will profile the metabolome, lipidome and proteome of tagged lysosomes purified from fibroblasts of patients with Alzheimer’s disease and Parkinson’s disease, and we will determine the biochemical basis of lysosomal dysfunction in these disorders.
Aim 3: We will determine the consequences of the lysosomal changes we discover in order to understand the biochemical basis of neurotoxicity in Alzheimer’s disease and Parkinson’s disease. Using functional approaches, we will determine the role of altered lysosomal pathways in disease pathology.
Developmental research project (2020) 1.2
Principal investigator: Heather E. Moss, MD, PhD
Title: Retinal biomarkers of Alzheimer’s disease and related diseases
Project description: Development of effective therapies for Alzheimer’s disease and related diseases has been hampered by lack of biomarkers to facilitate early diagnosis of disease and measure early treatment response. The retina is a promising tissue in which to identify biomarkers of neurological diseases because the retina is comprised of neural tissue and can be imaged non-invasively in vivo with high resolution. Historical attempts to leverage in vivo imaging derived retinal measurements in patients with neurological diseases for clinical advantage has been stymied by lack of specificity, which we believe is due to low resolution of clinical retinal imaging modalities. Accordingly, this application seeks to apply state-of-the-art retinal imaging technology to discover features in the retinas of human subjects with mild cognitive impairment and Alzheimer’s disease that can be developed as biomarkers for early detection of Alzheimer’s disease and measurement of Alzheimer’s disease progression. We hypothesize that there are specific retinal changes associated with Alzheimer’s disease and that these can be detected using in-vivo ophthalmic imaging. Subjects with Alzheimer’s disease, mild cognitive impairment and healthy controls will undergo cellular-level retinal imaging with adaptive optics scanning laser ophthalmoscopy. Structural retinal features unique to Alzheimer’s disease and mild cognitive impairment subjects will be identified through comparison with control subjects. Categorical and continuous measures of retinal structural features will be correlated with baseline cognitive testing, neuroimaging and cerebrospinal fluid measures collected for Alzheimer’s disease and mild cognitive impairment subjects through the Alzheimer’s Disease Research Center as well as with changes in these measures during the year after retinal imaging. The immediate impact of this project will be to identify specific retinal features in living humans that are candidates for detection of neurodegeneration and progression of neurodegeneration in Alzheimer’s disease. The features will have direct translational potential as biomarkers that are relevant to human disease and practical for measurement in living humans. In the longer term these will serve as the foundation for new directions for Alzheimer’s disease research in humans, including developing interventions to prevent and treat Alzheimer’s disease.
