A brainwide atlas of synapses across the mouse life span

Abstract

Synapses connect neurons together to form the circuits of the brain, and their molecular composition controls innate and learned behavior. We analyzed the molecular and morphological diversity of 5 billion excitatory synapses at single-synapse resolution across the mouse brain from birth to old age. A continuum of changes alters synapse composition in all brain regions across the life span. Expansion in synapse diversity produces differentiation of brain regions until early adulthood, and compositional changes cause dedifferentiation in old age. The spatiotemporal synaptome architecture of the brain potentially accounts for life-span transitions in intellectual ability, memory, and susceptibility to behavioral disorders.

Figure 1. Lifespan trajectories of synapse parameters

A. PSD95-eGFP (green) and SAP102-mKO2 (magenta) expression acquired at low (20X, i and ii) and high (100X, iii) magnification in the whole brain (i), hippocampus (ii), and molecular layer of the dentate gyrus (iii) at ten ages across the mouse postnatal lifespan. Scale bars: i, 4 mm; ii, 500 μm; iii, 3.5 μm. D, day; W, week; M, month. B. Lifespan trajectories of synapse density, intensity (normalized to the mean intensity, arbitrary units: AU) and size in the whole brain. PSD95-eGFP (green) and SAP102-mKO2 (magenta). Points represent individual mice, with beta-spline smoothed curve of mean values and standard error of the mean. C. Differences (Cohen’s d) in synapse parameters between 3M and 18M in brain subregions (numbered, see Table S1). *P < 0.05, Bayesian test with Benjamini-Hochberg correction. CB: cerebellum, CTXsp: cortical subplate, HPF: hippocampal formation, HY: hypothalamus, MB: midbrain, MY: medulla, OLF: olfactory areas, P: pons, PAL: pallidum, STR: striatum, TH: thalamus.

Figure 2. Lifespan trajectories of synapse types, subtypes and diversity

A. Stacked bar plot of percentage of synapse type density (type 1, PSD95 only; type 2, SAP102 only; type 3, colocalized PSD95+SAP102) in the whole brain across the lifespan. B. Percentage of synapse subtype density in the whole brain across the lifespan. Key: synapse subtypes (–37). C. Percentage of synapse subtype density in hippocampus and cerebellum across the lifespan. D. Lifespan trajectories of synapse type (normalized) density in 12 regions and 109 subregions (rows, see Table S1). Density in each subregion was normalized (0-1) to its maximal density across the lifespan (columns). Twelve brain regions are shown (abbreviations as Fig. 1C). E. Lifespan trajectories of three representative synapse subtypes (2, 16, 31) in each of 109 subregions (rows) (see Table S1). Density in each subregion was normalized (0-1) to its maximal density across the lifespan (columns). F. Lifespan trajectories of synapse diversity (Shannon entropy) for whole brain (top) and main regions from the cerebrum (middle) and brainstem and cerebellum (bottom). Beta-spline smoothed curve of mean and standard error of the mean are shown. G. Unsupervised synaptome maps showing the spatial patterning of synapse diversity (Shannon entropy) per area (pixel size 21.5 μm x 21.5 μm) in representative para-sagittal sections (all ages available in Fig. S15 and website(8)).

Figure 3. Lifespan synaptome architecture

A. Matrix of similarities between pairs of subregions (rows and columns) at 1W, 3M and 18M (see Fig. S16 for all ages). Small white boxes indicate the subregions that belong to the same main brain region (see color code, left and top) and larger white boxes indicate main clusters: cerebrum, brainstem, cerebellum. Note reduction in similarity from 1W to 3M and increase to 18M. Iso, isocortex; other abbreviations as Fig. 1C. B. Similarity ratio compares the relative similarity of the synaptome in each main brain region with that of every other region(8). See Materials and Methods for details. Significant differences of ratio between 3M and other ages: **P < 0.01, ***P < 0.001; two-way ANOVA with post-hoc multiple comparison test. C. Whole-brain hypersimilarity matrix showing the similarity between pairs of subregions at all ages. White boxes indicate the three main clusters, which correspond to LSA-I, -II and -III. Yellow box shows increased similarity of the old brain with the young brain. D. Hippocampus hypersimilarity matrix showing the similarity of pairs of hippocampal subregions at all ages (higher magnification image in Fig. S18). White boxes indicate the three main clusters corresponding to LSA-I, -II and -III. Yellow box shows the increased similarity of the old brain with the young brain. E. Average small worldness across the lifespan. Scatter plots indicate the average small worldness per mouse brain section at different ages. Significant differences of small worldness between 3M and other ages: *P < 0.05, **P < 0.01, ***P < 0.001; two-way ANOVA with post-hoc multiple comparison test.

Figure 4. Lifespan changes in hippocampus architecture and electrophysiological properties

A. Schematics of hippocampus showing radial and tangential gradients in CA1sr subfields. Graphs show gradients of normalized synapse intensity (AU) of PSD95 and SAP102 at 1W, 3M and 18M. CA1: cornu ammonis 1, CA2: cornu ammonis 2, CA3: cornu ammonis 3, DG: dentate gyrus, gr: granular layer, mo: molecular layer, po: polymorphic cell layer, slm: stratum lacunosum-moleculare, slu: stratum lucidum, so: stratum oriens, sp: stratum pyramidale, sr: stratum radiatum. B. The summed response (EPSP amplitude) to three patterns (gamma, theta, theta-burst) of 20 action potentials of the 11 x 11 matrix of hippocampus synapses at three ages. Histograms show changes (summed Euclidean distance, ED) between 1W and 3M (purple), and 3M and 18M (yellow). C. Schematic of the flow of information (arrows) in the trisynaptic hippocampal circuit connecting DG molecular layer (DGmo), CA3 stratum radiatum (CA3sr) and CA1 stratum radiatum (CA1sr), and the lifespan trajectory of synapse subtype density (normalized) in each region. EC, entorhinal cortex.