The Brian Hafler Lab
Molecular pathways leading to neurodegeneration in human disease
A) A sketch of the human retina. The retina is a thin tissue that lies on the inner part of the eyeball that processes light into neural signals that are transmitted through the optic nerve to the brain. B) Age-related macular degeneration has an early dry stage where there is accumulation of drusen debris beneath the retina. Drusen lead to activation of the innate immune response and neuroinflammation. During the late advanced stage of age-related macular degeneration, pathological new blood vessel formation occurs that can lead to permanent vision loss through the death of photoreceptors. Accumulation of extracellular plaques and intracellular neurofibrillary tangles in Alzheimer's disease and myelin damage in progressive multiple sclerosis are similarly accompanied by microglia (blue) and astrocyte (orange) activation. C) In collaboration with Smita Krishnaswamy’s lab in the Department of Genetics and Computer Science, an algorithm diffusion condensation was developed and applied to new age-related macular degeneration single-cell data. This panels shows a visual description of the cellular condensation process undertaken by diffusion condensation across four granularities. Points are moved to and merged with their nearest neighbors as determined by a weighted random walk over the data graph. Over many successive iterations, cells collapse, denoting cluster identity at various iterations. D) The process described in (C) creates hundreds of granularities of clusters which can be analyzed in meaningful ways: i) we can visualize the hierarchy of clusters computed by diffusion condensation, to identify the merging behavior across granularities; ii) we can identify meaningful, persistent partitions of the data by performing topological activity analysis; iii) in conjunction with MELD, we can scan across these meaningful granularities to identify resolutions that optimally split disease-enriched populations of cells from healthy populations of cells and finally; iv) we can compute differentially enriched genes between populations of interest.This figure is adapted from (Kuchroo M, DiStasio M, Calapkulu E, Ige M, Zhang L, Sheth A, Menon M, Xing Y, Dhodhapkar R, Gigante S, Wolf G, Krishnaswamy D, Hafler BP.Topological analysis of single-cell data reveals shared glial landscape of macular degeneration and neurodegenerative diseases. bioRxiv 2021.01.01.19.427286) and generated in collaboration with the Krishnaswamy lab.
Our data (Menon et al., 2019 Nature Comm, Mathys et al. 2019 Nature, Kuchroo et al., 2021, bioRxiv) based on single cell analysis of healthy retinas and diseased retinas with macular degeneration and glaucoma indicate that the key inflammatory pathways reside in specialized glial cells known as astrocytes, Muller glia, and microglia. Our novel machine learning pipeline identified neuroinflammatory cytokines that promote disease progression, cause vision loss, and provide a genetic context to target these cell types and signaling pathways as a novel disease therapeutic to prevent vision loss in people suffering from these diseases. Most of our research is performed using human tissue, mouse, and glial cell cultures.