My lab uses a multidisciplinary approach including multi-omic analysis, human induced pluripotent stem cell platform, and systems neuroscience approach, to investigate aging and Alzheimer’s disease (AD) and related dementias, and explores novel therapeutic approaches for preventing neuronal demise and ameliorating cognitive decline. Using epigenomic analyses on the CK-p25 neurodegneration mouse model, we discovered important contributions of dysregulated innate immune response genes to the neurodegeneration phenotype, similar to observations in human AD patients (Gjoneska et al, 2015). We further identified heterogeneous microglia populations in CK-p25 mice using single cell RNA-sequencing (scRNA-seq) (Mathys et al, 2017). By applying high throughput scRNA-seq analysis to postmortem brain samples from individuals with different degrees of AD, we identified distinct subpopulations for all major brain cell types and observed subtype-specific gene expression changes related to AD pathology (Mathys et al, 2019). These gene expression changes affected predominantly myelination-related processes and, intriguingly, differed between male and female cells. To investigate cell-type specific phenotypes related to AD or other neurological diseases further, we turned to cell-culture models based on patient-derived induced pluripotent stem cells (iPSC). The Picower Institute’s iPSC facility, which I co-founded and now oversee, can generate all major brain cell types including neurons, microglia, astrocytes, oligodendrocytes, pericytes, and brain endothelial cells. We used cells differentiated from patient-derived isogenic iPSC lines together with isogenic controls generated by CRISPR/Cas9 editing to demonstrate that APOE4, a major AD risk factor, impacts multiple brain cell types in different ways to promote the development of AD-related pathology (Lin et al, 2018). In iPSC-derived astrocytes, APOE4 led to disruption of the cellular lipidome and accumulation of intracellular lipid droplets, changes that could be rescued by supplementation with the phospholipid precursor choline (Sienski et al, 2021). To identify the effect of APOE4 on the brain-blood barrier (BBB), we assembled an “iBBB” model from iPSC-derived astrocytes, brain epithelial cells, and pericyte-like mural cells and systematically varied the genotype of each cell type within the iBBB. These studies revealed pericytes as the cell type responsible for APOE4-associated cerebral amyloid angiopathy (Blanchard et al, 2020). Using iPSC-derived microglia and neurons, we were able to show that APOE4 microglia also accumulate intracellular lipid droplets and then no longer support, but rather disrupt network activity between co-cultured neurons (Victor et al, 2022). Since our scRNA-seq results indicated changes to signaling pathways associated with cholesterol homeostasis and transport in oligodendrocytes with APOE4, we further generated an in-vitro myelination model with iPSC-derived oligodendrocytes and neurons. Using this model, we showed that oligodendrocytes with APOE4 accumulate aberrant cholesterol deposits and have reduced myelination activity (Blanchard et al, 2022). Importantly, the combination of our big-data approach and our in-vitro model systems has allowed us to identify pharmacological interventions tailored to cell type and pathology such as cyclosporine A/FK506 for reducing amyloid deposits in pericytes, choline supplementation for preventing lipid accumulation in astrocytes, and cyclodextrin for resolving cholesterol deposits in oligodendrocytes and improving their myelination activity. In an ongoing project, we are optimizing the assembly of an entire vascularized “brain on a chip” from the different iPSC-derived brain cell types. This multicellular integrated “miBrain” system will be used both for mechanistic studies and as an ex-vivo drug screening platform. Another major current interest in my lab is characterization of the effects that gamma oscillation entrainment in the brain has on brain pathologies associated with different neurodegenerative diseases. Following the initial demonstration that light-activated channels can activate and inactivate neuronal firing, my lab was one of the first to take advantage of optogenetics to manipulate neurocircuits. In collaboration with Christopher Moore and Jessica Cardin, we used adeno-associated virus (AAV) expressing channelrhodopsin 2 (ChR2) to drive fast-spiking parvalbumin (PV)-positive interneurons in mouse somatosensory cortex and found that this stimulation induces gamma oscillations and modulates sensory responses (Cardin et al, 2009). These results prompted us to test the effect of induced gamma oscillations in AD model mice, which show impaired endogenous gamma. We found that entraining gamma oscillations in these mice with optogenetics or with a non-invasive flickering light led to a marked reduction in beta-amyloid peptide levels (Iaccarino et al, 2016). My lab subsequently showed that Gamma ENtrainment Sensory stimuli (GENUS) using several weeks of daily auditory stimuli or simultaneous visual and auditory stimuli impacted multiple brain cell types - including neurons, microglia, astrocytes, and the vascular compartment - and reduced multiple AD pathologies, such as amyloid, phosphorylated tau, and neuronal and synaptic loss (Adaikkan et al, 2019, Martorell et al, 2019). Reduction of AD-related pathology occurred not only within the primary sensory cortex, but also in the hippocampus memory center and the prefrontal cortex and was accompanied by improved memory functions in treated model mice. We are currently investigating effects of GENUS in models of other neurodegenerative diseases, including multiple sclerosis, Parkinson’s disease, Down syndrome, and chemobrain, as well as GENUS effects outside of the brain, such as in the peripheral components of the brain-gut axis.     Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai L-H, Kellis M. (2015) Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature 518, 365-9. Mathys H, Adaikkan C, Gao F, Young JZ, Manet E, Hemberg M, De Jager PL, Ransohoff RM, Regev A, Tsai L-H.(2017) Temporal tracking of microglia activation in neurodegeneration of single-cell resolution. Cell Rep 21(2), 366-380. Mathys H, Davila-Velderrain J, Peng Z, Gao F, Mohammadi S, Young JZ, Menon M, He L, Abdurrob F, Jiang X, Martorell AJ, Ransohoff RM, Hafler BP, Bennett DA, Kellis M, Tsai L-H. (2019) Single-cell transcriptomic analysis of Alzheimer’s disease. Nature 570, 332-337. Lin YT, Seo J, Gao F, Feldman HM, Wen H, Penney J, Cam HP, Gjonetska E, Raja W, Cheng J, Rueda R, Kritskiy O, Abdurrob F, Peng Z, Milo B, Yu CJ, Elmsaouri S, Dey D, Ko T, Yankner B and Tsai L-H. (2018) APOE4 causes widespread molecular and cellular alterations associated with Alzheimer’s disease phenotypes across human iPSC-derived brain cell types. Neuron, 2018 Jun 27; 98 (6):1294. Sienski G, Narayan P, Bonner JM, Kory N, Boland S, Arczewska AA, Ralvenius WT, Akay L, Lockshin E, He L, Milo B, Graziosi A, Baru V, Lewis CA, Kellis M, Sabatini DM, Tsai L-H, Lindquist S. (2021). APOE4 disrupts intracellular lipid homeostasis in human iPSC-derived glia. Science Translational Medicine 13(583), eaaz4564. Blanchard JW, Bula M, Davila-Velderrain J, Akay LA, Zhu L, Frank A, Victor MB, Bonner JM, Mathys H, Lin Y-T, Ko T, Bennet DA, Cam HP, Kellis M, Tsai L-H. (2020) Reconstruction of the human blood-brain barrier in vivo reveals a pathogenic mechanism of APOE4 in pericytes. Nature Medicine 26, 952-963. Victor MB, Leary N, Luna X, Meharena HS, Bozzelli PL, Samaan G, Murdock MH, von Maydell D, Effenberger AH, Cerit O, Wen H-L, Liu L, Welch G, Bonner M, Tsai L-H (2022) Lipid Accumulation Induced by APOE4 Impairs Microglial Surveillance of Neuronal-Network Activity. Cell Stem Cell 29:1197-1212.e8. Blanchard JW, Akay LA, Davila-Velderrain J, von Maydell D, Mathys H, Davidson SM, Effenberger A, Chen CY, Maner-Smith K, Hajjar I, Ortlund EA, Bula M, Agbas E, Ng A, Jiang X, Kahn M, Blanco-Duque C, Lavoie N, Liu L, Reyes R, Lin YT, Ko T, R'Bibo L, Ralvenius WT, Bennett DA, Cam HP, Kellis M, Tsai LH (2022) APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes. Nature Nov 16. Epub ahead of print. Cardin JA, Carlén M, Meletis K, Knoblich U, Zhang F, Deisseroth K, Tsai L-H, Moore CI. (2009) Driving fast-spiking cells induces gamma rhythm and controls sensory responses. Nature 459(7247), 663-7. Iaccarino HF, Singer AC, Martorell AJ, Rudenko A, Gao F, Gillingham TZ, Mathys H, Seo J, Kritskiy O, Abdurrob F, Adaikkan C, Canter RG, Rueda R, Brown EN, Boyden ES, Tsai L-H. (2016) Gamma frequency entrainment attenuates amyloid load and modifies microglia. Nature 540(7632), 230-235.  Martorell AJ, Paulson AL, Suk  H-J, Abdurrob F, Drummon G, Guan W, Young JZ, Kim D, N-W, Kritskiy O, Barker S, Mangena V, Brown EN, Chung K, Boyden ES, Singer AC, Tsai L-H. (2019) Multi-sensory gamma stimulation ameliorates Alzheimer's-associated pathology and improves cognition. Cell 177(2), 256-271. Adaikkan C, Middleton SJ, Marco A, Pao P-C, Mathys H, Kim DN-W, Gao F, Young JZ, Suk H-J, Boyden ES, McHugh TJ, Tsai L-H. (2019) Gamma Entrainment Binds Higher-Order Brain Regions and Offers Neuroprotection. Neuron 102(5): 929-943.