BioProject

In this study, we characterize the transcriptomic alterations, cellular compositions, and signaling perturbations in the amyloid plaque niche in an AD mouse model using high-resolution spatial transcriptomics (CosMx and Stereo-seq). More...

In this study, we characterize the transcriptomic alterations, cellular compositions, and signaling perturbations in the amyloid plaque niche in an AD mouse model using high-resolution spatial transcriptomics (CosMx and Stereo-seq). We discover a wide heterogeneity in the cellular composition of amyloid plaque niches, marked by an increase in microglial accumulation over time. We profile the alterations of glial cells as they are exposed to plaques, and conclude that the microglial response to plaques is consistent across different brain regions, while the astrocytic response is more heterogeneous. In turn, as the microglial density of plaque niches increases, astrocytes acquire a more neurotoxic phenotype and play a key role in inducing GABAergic signaling and decreasing glutamatergic signaling in neurons of the hippocampus. Taken together, we show that astrocytic signaling around plaque pathology is disrupted with increasing microglial density, which in turn induces an imbalance in synaptic signaling in neurons in the hippocampus. Overall design: Stereo-seq technology was applied to coronal sections of AppNL-G-F KI and C57BL/6J background mice at 3 and 18 months of age. Two mixed hemispheres, where one hemisphere is from a WT mouse and the other from an AppNL-G-F mouse, were processed for 3M animals, whilst two full coronal sections were processed for the 18M AppNL-G-F mice, with one full coronal section of an age-matched control. Briefly, 10 µm thick tissue sections were fixed to Stereo-seq chips, with immediately adjacent slides collected for staining. The sections were then stained for ssDNA and imaged to obtain nuclei location information. Tissue sections were then permeabilized and reverse transcription was performed overnight. Afterwards, tissue was digested and cDNA released from the chip. The recovered cDNA was amplified and fragmented for library construction. PCR products were purified and sequenced on a MGI DNBSEQ-Rx sequencer. Adjacent slides from the Stereo-seq experiments were stained using a standard IHC protocol to visualize reactive astrocytes and amyloid-β plaques. 16-bit fluorescent images of DAPI, 6E10, and GFAP were acquired on a Zeiss Axioscan.Z1 slidescanner. Different FOV were stitched together. The Stereo-seq raw data processing was performed in publicly available SAW pipeline (https://github.com/BGIResearch/SAW). In brief, fastq files were generated using a MGI DNBSEQ-Tx sequencer.Reads passing QC metrics were aligned to the mm10 reference genome using STAR. Mapped reads with MAPQ > 10 were counted and annotated to their corresponding genes, resulting in a CID-containing expression profile matrix. Less...