Methodology.

a) Illustration of the partial least squares correlation analysis. Starting from two input matrices containing per-subject information of regional morphological measures as well as clinical data (demographic and MetS-related risk factors) a correlation matrix is computed. This matrix is subsequently subjected to singular value decomposition resulting in a set of mutually orthogonal latent variables. Latent variables each consist of a left singular vector (here, clinical covariance profile), singular value and right singular vector (here, imaging covariance profile). In addition, subject-specific clinical and imaging scores are computed. b) The interplay between MetS, brain structure and cognition was investigated in a post-hoc mediation analysis. We tested whether the relationship between the clinical score, representing MetS severity, and different cognitive test performances was statistically mediated by the imaging score. c) Contextualization analysis. Upper row: based on microarray gene expression data, the densities of different cell populations across the cortex were quantified. Middle and lower row: based on functional and structural group-consensus connectomes based on data from the Human Connectome Project, metrics of functional and structural brain network topology were derived. Cell density as well as connectomic measures were related to the bootstrap ratio via spatial correlations. Modified from Petersen et al. and Zeighami et al. [33,82].

Abbreviations: Astro – astrocytes; DWI – diffusion-weighted magnetic resonance imaging; Endo – endothelial cells; Ex – excitatory neuron populations (Ex1-8); In – inhibitory neuron populations (In1-8); Micro – microglia; Oligo – oligodendrocytes; rs-fMRI – resting-state functional magnetic resonance imaging; SVD – singular value decomposition.

Descriptive statistics UKB and HCHS

Partial least squares (PLS) analysis.

a) Explained variance and p-values of latent variables. b) Scatter plot relating subject-specific clinical and imaging PLS scores. Higher scores indicate higher adherence to the respective covariance profile. c) Clinical covariance profile. 95% confidence intervals were calculated via bootstrap resampling. Note that confound removal for age, sex, education and cohort was performed prior to the PLS. d) Imaging covariance profile represented by bootstrap ratio. A high positive or negative bootstrap ratio indicates high contribution of a brain region to the overall covariance profile. Vertices with a significant bootstrap ratio (> 1.96 or < ™1.96) are highlighted by colors. Abbreviations: - Spearman correlation coefficient.

Mediation analysis results.

Mediation effects of subject-specific imaging PLS scores on the relationship between MetS represented by the clinical PLS score and cognitive test performances. Path plots display standardized effects and p-values: (a) clinical score to imaging score, (b) imaging score to cognitive score, (ab) indirect effect (c’) direct effect and (c) total effect. Significant paths are highlighted in blue; non-significant in light gray. If the indirect effect ab was significant, the text for ab is highlighted in blue. A blue dot in the path plot indicates if a relationship is significantly mediated, i.e., the indirect effect ab was significant and the direct effect c’ was reduced or non-significant compared to the total effect c. An empty dot indicates a partial mediation, a full dot indicates a full mediation. Abbreviations: - false discovery rate-corrected p-values; PLS – partial least squares correlation; TMT-A – Trail Making Test A; TMT-B – Trail Making Test B.

Virtual histology analysis.

The correspondence between MetS effects (bootstrap ratio) and cell type-specific gene expression profiles was examined via an ensemble-based gene category enrichment analysis. a) Barplot displaying spatial correlation results. The bar height displays the significance level. Colors encode the aggregate z-transformed Spearman correlation coefficient relating the Schaefer100-parcellated bootstrap ratio and respective cell population densities. Asterisks indicate statistical significance. The significance threshold of <.05 is highlighted by a vertical dashed line. b) Scatter plots illustrating spatial correlations between MetS effects and exemplary cortical gene expression profiles per cell population significantly associated across analyses – i.e., endothelium, microglia and excitatory neurons type 8. Top 5 genes most strongly correlating with the bootstrap ratio map were visualized for each of these cell populations. Icons in the bottom right of each scatter plot indicate the corresponding cell type. A legend explaining the icons is provided at the bottom. First row: endothelium; second row: microglia; third row: excitatory neurons type 8. Virtual histology analysis results for the bootstrap ratios of latent variables 2 and 3 are shown in supplementary figure S21. A corresponding plot illustrating the contextualization of the t- statistic derived from group statistics is shown in supplementary figure S22. Abbreviations: −log(pFDR) – negative logarithm of the false discovery rate-corrected p-value derived from spatial lag models [36,41]; r – Spearman correlation coeffient. Z(rsp) – aggregate z- transformed Spearman correlation coefficient.

Brain network contextualization.

Spatial correlation results derived from relating Schaefer400×7-parcellated maps of MetS effects (bootstrap ratio) to network topological indices (red: functional connectivity, blue: structural connectivity). Scatter plots that illustrate the spatial relationship are supplemented by respective surface plots for anatomical localization. The color coding of cortical regions and associated dots corresponds. a) & b) Functional and structural degree centrality rank. c) & d) Functional and structural neighborhood abnormality. e) & f) Intrinsic functional network hierarchy represented by functional connectivity gradients 1 and 2. Complementary results concerning t-statistic maps derived from group comparisons between MetS subjects and controls are presented in supplementary figure S24. Corresponding results after reperforming the analysis with HCHS derived group-consensus connectomes are presented in supplementary figure S25. Abbreviations: HCHS – Hamburg City Health Study; prewire - p-value derived from network rewiring [47]; psmash - p-value derived from brainSMASH surrogates [46]; pspin - p-value derived from spin permutation results [45]; rsp - Spearman correlation coefficient.