NHGRI Advanced Imaging & Analysis Core

National Human Genome Research Institute

Investigators

Linked publications, trials & patents

Abstract

Summary: In total, 2,602 hours of microscopy experiments were conducted from Oct. 1, 2024, to Aug. 27, 2025, utilizing any of the eight microscope systems or two processing workstations available at the Advanced Imaging & Analysis Core Facility (AIACF) to support the NHGRI scientific community. There were 38 unique users of the core from 16 different NHGRI labs. The AIACF provided training for investigators and trainees on using Confocal Laser Scanning Microscopy for studies involving Fluorescence Recovery After Photo-bleaching (FRAP), Fluorescence Resonance Energy Transfer (FRET), Photo-activation of Green Fluorescent Protein (PA-GFP), nuclear/organelle/cytoplasmic colocalization, and Two-Dimensional (2D), Three-Dimensional (3D), and Four-Dimensional (4D) cell morphology. Analyses included volumetric studies, response to stimuli (drug), quantitative analysis (e.g. intensities, areas, counts, morphologies, etc.), and incorporating AI protocols to ease analysis fatigue. AIACF also trained users in high-content imaging, live-cell imaging, slide scanning for digitizing slide libraries, and super-resolution microscopy (STORM technique). Microscopy usage was measured by the hours logged by Principal Investigators or their trainees. The Core maintains two confocal systems (Zeiss LSM 880 + Airyscan and Spinning disk), one long-term live-cell system, one automated slide scanner, one automated high-content imager, one super-resolution system, and two epi-fluorescence microscopes with CCD cameras, as well as two computer workstations. Below is an abbreviated list of projects the Core collaborated on over the past year: Dr. Gahl’s laboratory (MGB) investigates lysosomal and lysosome-related organelle disorders, with a particular focus on Free Sialic Acid Storage Disorder (FSASD). FSASD is a rare, autosomal recessive neurodegenerative lysosomal storage disorder caused by biallelic variants in SLC17A5, which encodes sialin, a lysosomal transmembrane protein responsible for exporting free sialic acid from lysosomes to the cytosol. Patients exhibit a multisystemic phenotype, including progressive neurodegeneration and pronounced CNS hypomyelination. While sialin’s function in lysosomal transport is established, its role in neuronal and glial biology—particularly in myelination—remains poorly understood. To address this gap, the lab generated a novel Slc17a5^R39C knock-in mouse model harboring the most prevalent pathogenic patient variant (p.Arg39Cys). Using the advanced imaging capabilities of our institute’s Microscopy Core, the lab applies immunofluorescence microscopy and histopathological imaging to spatiotemporally characterize neurodegenerative and myelination processes in mutant and wild-type murine tissues. Microscopy enables precise labeling and quantification of glial precursors and differentiated glia during key stages of CNS development, providing critical insight into the cellular dynamics underlying hypomyelination. Parallel efforts focus on cerebellar Purkinje cell degeneration, where high-resolution imaging allows tracking of morphology, dendritic architecture, and progressive cell loss across developmental timepoints and cerebellar regions. These microscopy-based approaches are further applied to assess therapeutic outcomes, including evaluating glial responses and neuronal preservation following experimental gene therapy interventions in the SLC17A5^R39C model. By leveraging advanced imaging and the resources of the Microscopy Core, the lab integrates cellular and molecular analyses to define the pathophysiology of FSASD and identify imaging biomarkers that can inform therapeutic strategies. Ultimately, microscopy is central to the lab’s mission of uncovering targetable pathological mechanisms in myelination deficits and neurodegeneration, with the long-term goal of improving treatment approaches for FSASD. Dr. Loftus’s research within the Gahl Lab is seeking to establish an automated assay for interrogation of variants of unknown significance (VUSs) that have been identified in individuals with oculocutaneous albinism. This project has utilized the DeltaVision, wide view microscope to allow for visualization of both fluorescent of and brightfield images of hundreds of melanocyte vesicles across the entirely of a melanocyte cell. The core has been instrumental in modifying the computational tools to allow for an automated identification of transfection-positive melanosomes and provide for automated quantification of the amount of corrected melanin produced by each oculocutaneous albinism gene variant queried. Dr. Liu’s lab (TFGB) - In 2019, our group launched a longitudinal natural history study of patients with germline RUNX1 variants to increase our understanding of familial platelet disorder (FPD), which will hopefully lead to better clinical management and potentially new therapies. We have been characterizing in vitro the pathogenicity of RUNX1 variants identified in our patients using different functional assays, which include immunofluorescence staining and imaging by confocal microscopy. We aim to determine the subcellular localization of RUNX1, which should be in the nucleus, as well as its binding partner CBFβ, a cytoplasmatic protein that translocates to the nucleus when interacting with RUNX1. The NHGRI Advanced Imaging & Analysis core facility has been fundamental for our study, as it provide us with the technology to perform these assays, as well as the analysis software and technical support to analyze and interpret the microscopy data. Dr. McGuire’s lab (MMB) – The McGuire lab is using the confocal microscope to check the expression status of different sialic acid marker in mouse lung tissue and mouse lung derived cell line LET1 cells. To investigate sialic acid levels, specific lectins that bind to sialic acids are employed. In particular, Maackia amurensis agglutinin (MAA), Sambucus nigra agglutinin (SNA), and Peanut agglutinin (PNA) are commonly used. MAA preferentially binding to α2,3-linked sialic acids and SNA to α2,6-linked sialic acids. PNA, on the other hand, binds specifically to the Galβ1-3GalNAc sequence, which can be unmasked upon sialic acid removal. In these experiments we are using these lectin probes for studying the complex glycosylation patterns in lung tissue, aiding in the investigation of various pathological conditions such as Influenza virus infection in wild type and NDUFS4 KO mice. Use of confocal microscope provides the advantage of optical sectioning, enabling detailed analysis of specific layers and cellular compartments within the tissue. This technique also provides a detailed analysis of overall Sialic acid expression in infected as well as non-infected cells. McGuire lab is also using spinning disk confocal microscopy to investigate the subcellular localization of ATP sensor in wild-type (WT) cells under a range of physiological and stress-related conditions. To accurately determine the spatial distribution of the sensor, they co-stained cells with a variety of organelle-specific marker dyes such as those for mitochondria, endoplasmic reticulum, lysosomes, lipid droplets and nucleus. This approach enabled high-resolution, live-cell imaging with minimal phototoxicity, allowing to monitor dynamic changes in ATP localization. The data generated will help elucidate how ATP distribution is regulated across different cellular compartments in response to changing cellular environments. Dr. Giniger’s lab (Adjunct MGB) in the Axon Guidance and Neural Connectivity Section of NINDS has two general groups of projects that we perform in the NHGRI AIACF. One portion of the lab studies how nerves grow during early nervous system development. The focus of these experiments is to image individual axons as they grow in living tissue, tracking their structure, dynamics, and the activity of the molecules that promote and guide their growth. The other half of the lab studies the mechanisms of neurodegenerative disease and their association with aging. A major focus in this project is to use imaging of fluorescent reporters to quantify how the internal state of a neuron changes as it progresses over the course of disease. In both projects, technology that increases our resolution would allow us to ask entirely new questions. This includes increase of temporal resolution to follow fast dynamics of subcellular structures and increase of spatial resolution to distinguish between features in the tightly-packed neuronal cytoplasm. Dr. Sidransky’s lab (MGB) is investigating the link between glucocerebrosidase (encoded by GBA1) and the development of Parkinson disease. Heterozygote variants in the gene GBA1 are the most common genetic risk factor for Parkinson disease. Homozygous mutations in GBA1 cause the lysosomal storage disorder Gaucher disease, but despite carrying biallelic mutations, only a minority of patients with Gaucher disease develop Parkinson disease. To understand the molecular differences between individuals who develop the neurodegenerative disorder from those who are spared, we use iPSCs. We have generated both patient-derived isogenic iPSC lines engineered to carry different GBA1 variants, in addition to wt and knockout genotypes. We have also generated iPSC lines from siblings with Gaucher disease who are discordant for Parkinson disease. Using CRISPR we genetically engineered the iPSCs to optimize differentiation into glutamatergic and dopaminergic neurons. We are also working with murine models of glucocerebrosidase deficiency. We employ high content imaging to screen different potential small molecule pharmacologic chaperones at different concentration. Dr. Biesecker’s lab (CPHR) is utilizing the resources of the NHGRI Advanced Imaging & Analysis Core Facility to support multiple lines of investigation into the pathophysiology and potential therapeutic approaches to Hutchinson-Gilford Progeria Syndrome. The Axioscan slide scanner has enabled detailed histologic studies on multiple tissues from HGPS mouse models, including demonstration of decreased trabecular volume and abnormal growth plate structure in long bones of two mouse models of progeria, as characterized in a manuscript in preparation. These analyses have also confirmed improvements in bone, vascular and skin structural parameters in HGPS mice treated with a DNA base editor that corrects the mutation in vivo. To continue the gene therapy study on progeria, the lab conducted an extensive investigation on iPSC-derived vascular smooth muscle cells (VSMCs), a clinically relevant cell type in patients with HGPS. Microscopy studies showed improvement of nuclear morphology in ABE-corrected progeria VSMCs compared to WT control. Furthermore, confocal imaging of immunofluorescent staining of HGPS cell lines has illustrated improvements in nuclear structure following DNA base editor treatment in HGPS cell cultures in vitro, which is critical preclinical data required for our proposed FDA IND application.