Human Alzheimer’s postmortem raphe brain heterogeneity: Single cell RNAseq 10X genomics approach

Abstract

AbstractBackgroundThe complexity of subcortical brain remains unexplored due to complex neuronal structure and heterogeneity of neuronal populations in the brain. Raphe brain regulates multiple physiological events like stress, memory, feeding, sleep, movement, balance, and many others. ere we present the single cell RNAsec (scRNAseq) analysis of raphe tissue from the postmortem brains of Alzheimer’s disease Braak Stages VI and control subjects.MethodPostmortem raphe brains acquired from NIH‐NeuroBioBank. Intact cells were collected using Cell Raft AIR System. Single cell suspension of neurons and synthesized cDNA and normalized cDNA using library preparation. The samples were processed in NextGen v3‐1 using 10X Genomics Chromium system. The library was sequenced ± 200 million PE150 reads /sample on Illumina Novaseq. The sequences were mapped against GRCh38 using Cell ranger v6.1.ResultThe data will be analyzed using 10X genomics cell ranger and Loup Browser tools. Further functional genomics tool DAVID ) v6.8 and ( IPA ) will be used to analyze heterogeneity of raphe brain and various presynaptic neuronal modulation in 1. AD and control, 2. AD and control males and 3. AD and control females. The most astringent analysis of data showed 5% mitochondrial genes, . We will also analyze the therapeutic targets and biological pathways. Heterogeneity of raphe and genes triggered in AD pathology will also be investigated.ConclusionThe raphe connectivity to Alzheimer’s disease and other dementias was a hot‐topic in 1980s research and somehow lost interest in the last 2 decades. The concept of serotonin neuromodulation evolves in recent years due to new concept of serotonin connecting intracellular and intracellular neuromodulation, use of serotonin drug targets in behavior alterations in dementia and early depression and aggression might be a causal factor to neurodegenerative onset much before classic pathologies of the disease appear. Our study will reveal the heterogenous neuronal population in complex raphe region of the brain and how the microenvironment changes neurotransmission in the forebrain. We will present extensive analysis on neuronal population of raphe and its role in AD and healthy subjects. The results will be a AD and ADRD models to pinpoint the changes in 5HTsynthesis and neuromodulation to forebrain and cerebellum.