Structural Basis of Large-Scale Functional Connectivity in the Mouse

Abstract

Translational neuroimaging requires approaches and techniques that can bridge between multiple different species and disease states. One candidate method that offers insights into the brain's functional connectivity (FC) is resting-state fMRI (rs-fMRI). In both humans and nonhuman primates, patterns of FC (often referred to as the functional connectome) have been related to the underlying structural connectivity (SC; also called the structural connectome). Given the recent rise in preclinical neuroimaging of mouse models, it is an important question whether the mouse functional connectome conforms to the underlying SC. Here, we compared FC derived from rs-fMRI in female mice with the underlying monosynaptic structural connectome as provided by the Allen Brain Connectivity Atlas. We show that FC between interhemispheric homotopic cortical and hippocampal areas, as well as in cortico-striatal pathways, emerges primarily via monosynaptic structural connections. In particular, we demonstrate that the striatum (STR) can be segregated according to differential rs-fMRI connectivity patterns that mirror monosynaptic connectivity with isocortex. In contrast, for certain subcortical networks, FC emerges along polysynaptic pathways as shown for left and right STR, which do not share direct anatomical connections, but high FC is putatively driven by a top-down cortical control. Finally, we show that FC involving cortico-thalamic pathways is limited, possibly confounded by the effect of anesthesia, small regional size, and tracer injection volume. These findings provide a critical foundation for using rs-fMRI connectivity as a translational tool to study complex brain circuitry interactions and their pathology due to neurological or psychiatric diseases across species.SIGNIFICANCE STATEMENT A comprehensive understanding of how the anatomical architecture of the brain, often referred to as the "connectome," corresponds to its function is arguably one of the biggest challenges for understanding the brain and its pathologies. Here, we use the mouse as a model for comparing functional connectivity (FC) derived from resting-state fMRI with gold standard structural connectivity measures based on tracer injections. In particular, we demonstrate high correspondence between FC measurements of cortico-cortical and cortico-striatal regions and their anatomical underpinnings. This work provides a critical foundation for studying the pathology of these circuits across mouse models and human patients.

Keywords: functional connectome; mouse; resting-state fMRI; structural connectivity; viral tracing.

Figure 1.

ICA revealed the presence of robust resting-state networks in the mouse brain. Optimized MR acquisition, anesthesia and handling, and image-processing protocols yielded readily defined isocortical, striatal, thalamic, and hippocampal rs-fMRI networks.

Figure 2.

Qualitative comparison between tracer distribution indicating SC (green; top) and FC pattern derived from rs-fMRI (red; bottom) for four selected injection sites/seeds. The results illustrate a high degree of similarity between the measurements, particularly in ipsilateral cortico-striatal connectivity. A high degree of overlap was also found in contralateral cortico-cortical and hippocampalo-hippocampal connections, whereas cortico-thalamic anatomical projections were not detected by rs-fMRI.

Figure 3.

Comparison of the viral tracer connectivity matrix (a) and the corresponding FC matrix (b) from 238 seed-injection sites (see Fig. 3-2) by 254 target ROIs reveals striking similarities, in particular regarding the interactions within the isocortex. Partial Spearman's ρ (corrected for target ROI volume) between structural and functional connections originating from each seed/injection experiment is displayed in c and show weak-to-intermediate (rho: 0.2–0.4) and average-to-strong (rho: 0.4–0.6) correlations for most of the cortical, hippocampal, and striatal seeds (colors encode for regions as shown in a and b). Conversely, we were able to detect injection areas for which the SC-FC correlation dropped to nonsignificant levels (rho: 0–0.2), notably, for injection sites in prefrontal areas (ACAd, PL, ILA, ORBI), CA1, STR, amygdala, and some thalamic nuclei, which may be driven by the relatively small volume injected and by the absence of reciprocal projections between these and other brain regions (see Fig. 3-1). ROC curves are shown for connectivity of isocortex → isocortex (d; dashed square boxes), isocortex ↔ STR (e; black square boxes), and isocortex ↔ TH (f; dotted square boxes). The AUC indicates the degree of similarity between the structural and functional metrics, ranging from 0.5 (chance level) to 1 (full similarity). Permutation testing confirmed the significant (>chance level distribution) agreement between SC and FC in all the macroscale connections, with medium to high (>0.7) AUC levels for isocortex to its contralateral counterpart and for isocortex to STR and low (<0.6) for isocortical to thalamic connections (see Fig. 3-3).

Figure 4.

Winner-takes-all analysis for 20 injection sites/seeds located in the isocortex. a, Location of injection sites/seeds used for the winner-takes-all analysis mapped on a surface representation of the mouse isocortex. The labels are as follows: (1) MOs, (2) ORBm, (3) PL, (4) MOs, (5) MOp, (6) primary somatosensory area of the barrel field (SSp-bfd), (7) MOp, (8) ACAd, (9) SSs, (10) SSp-bfd, (11) SSp-ll, (12) AUDd, (13) PTLp, (14) AUDd, (15) RSPagl, (16) AUDd, (17) VISp, (18) VISp, (19) VISp, and (20) VISp. Two spheres of different diameters and transparency are drawn in each voxel, indicating the first and second strongest connected injection sites/seeds originating from the isocortex toward contralateral isocortex (b), ipsilateral STR (c), and ipsilateral TH (d). Voxel-based Spearman's r correlation indicates significant correlation between tracer injection and rs-fMRI data. Voxels from both isocortical and striatal maps present significant correlation (86.9% and 87.8% of total voxels, respectively) between structural and FC. In contrast, thalamic map presents a significant correlation between the two modalities in 8.8% of the voxels only, specifically in the anteroventral and ventral posteromedial nuclei of the TH.

Figure 5.

Distance separating node pairs from structural and FC at varying matrix threshold revealed a similar distribution (a,b). Structural and functionally connectivity matrices were normalized to a range of 0–100. Distance was computed for both matrices with incremental threshold with step size = 1. At a lower threshold, the number of edges separating any node pairs remains between one and two. The distance increases as threshold is increased. c, d, Distance analysis reveals monosynaptic or polysynaptic connectivity likelihood (CL) of FC. Large circular plots show transparency-coded links that represent CL for intrahemispheric (blue) and interhemispheric (red) connections across the brain. For the sake of clarity, intrahemispheric connections within brain structures are plotted outside and inside of the circle labeling the major brain regions (left side of graphs). Smaller circular plots indicate links between bilateral homotopic region pairs only. c, Isocortex presents balanced intrahemispheric and interhemispheric monosynaptic CL, toward HPF, CTXsp, and STR (intrahemispheric) and toward contralateral homotopic ROI (interhemispheric). d, Polysynaptic CL presents more diverse links between ROIs from different ontological structures and hemispheres, for example, STR to contralateral isocortex and STR. Polysynaptic homotopic interactions are found in the CTXsp, STR, PAL, and TH. Likelihood values are given as percentages. Mismatches between structural FC are shown in Figure 5-1.