GSE173955
Integrative analysis of altered genes expressed in human Alzheimer's disease brain (RNA-Seq)
We had previously performed comparative gene expression profiling of human postmortem Alzheimer's disease (AD) brains donated for the Hisayama study. The hippocampi from AD brains showed the most significant alteration in gene expression profile [PMID: 23595620]. In the present study, in order to identify molecular pathological alterations in AD hippocampus, we applied human transcriptome array and RNA-sequencing to the same samples and reanalyzed the gene array data, and performed integrative analysis of all 3 methods. We also applied gene array to hippocampus of 6-month-old AppNL-G-F/NL-G-F knock-in AD model mice as a preclinical AD stage model, and at last we performed the interspecies comparison. Functional annotation clustering with the results of all 3 or at least 2 methods in human, showed synapse, cell junction, calmodulin binding, ion transport and glycoproteins as the top affected terms. In hippocampi of AppNL-G-F/NL-G-F mice which exhibit significant amyloidosis but not neuronal degeneration, we found that expression of genes categorized in signaling specially signaling peptides with disulfide bond or glycoproteins, together with the innate immune response and lysosome of cells are upregulated. Comparing the extended human data with mouse data, we found and confirmed by qRT-PCR, 2 common up-regulated genes, Clec7a and C4b, which induce innate immune response and synapse elimination. We also found and confirmed by qRT-PCR, 2 common down-regulated genes, one is Slc17a6, which can affect synaptic transmission of glutamate, and second one is Rxfp1, which is involved in gene transcription. Amyloid-?? accumulation is the major hallmark of AD at 6 month-old AppNL-G-F/NL-G-F  mice, therefore our data suggests that amyloid-?? accumulation induces innate immune response, synapse elimination, besides it can decreases glutamate transmission, and affect gene transcription in early stage of hippocampal AD brain, prior to neuronal degeneration. Overall design: We analyzed postmortem human hippocampus brains from 8 AD and 10 non-AD subjects using Illumina TruSeq stranded mRNA LT Sample Prep kit. Sequences were obtained by using HiSeq1500. One AD and one non-AD sample applied two independent times to sequencer in order to obtain more reads.