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Aging and metabolism contribute separately to brain–body health

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Abstract

The brain and body undergo coordinated changes throughout the life span, yet studies of aging have traditionally examined these systems as separate entities. Here we ask how brain health relates to aging and peripheral biomarkers of metabolic and vascular function, including body mass index, blood pressure, and blood biochemistry. We use multivariate pattern learning to identify generalizable patterns of covariance between multi-modal neuroimaging data (structural, functional, diffusion, and arterial spin labeling MRI), demographic, and physiological markers in two large-scale deeply phenotyped datasets: the Human Connectome Project–Aging and UK Biobank. This data-driven approach isolates two principal axes of brain–body associations in both biological sexes. The first axis is driven by the dominant contribution of age. Across multiple brain measures, aging is associated with loss of brain structural integrity and cerebral vascular dysfunction. The second axis is driven by metabolic features, characterized by low high-density lipoprotein cholesterol, elevated body mass index, blood pressure, glycosylated hemoglobin, insulin, glucose, and alanine aminotransferase that predominantly converge on reduced cerebral perfusion. Importantly, the aging and the metabolic axes are independent of each other, meaning that age and metabolic dysfunction have separable influences on the brain. Finally, we show that deviations from a healthy metabolic profile are linked to cognitive deficits, particularly in females. Our study contributes to development of comprehensive translatable biomarkers for brain health assessment, and highlights the importance of metabolic health as a determinant of brain health in aging population.

Citation: Farahani A, Liu Z-Q, Morys F, Moqadam R, Zeighami Y, Dadar M, et al. (2026) Aging and metabolism contribute separately to brain–body health. PLoS Biol 24(6): e3003856. https://doi.org/10.1371/journal.pbio.3003856

Academic Editor: Claus C. Hilgetag, University Medical Center Hamburg-Eppendorf: Universitatsklinikum Hamburg-Eppendorf, GERMANY

Received: November 20, 2025; Accepted: June 1, 2026; Published: June 15, 2026

Copyright: © 2026 Farahani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: Due to the Human Connectome Project-Aging (HCP-A) and UK Biobank data sharing policy, the data used in this study could not be shared though authors of this paper. The HCP-A data are accessible through https://www.humanconnectome.org/study/hcp-lifespan-aging. The UK Biobank data are accessible through https://www.ukbiobank.ac.uk. All code used to perform the analyses and data underlying the main figures are available on GitHub at https://github.com/netneurolab/Farahani_Age_Metabolism and on Zenodo at https://zenodo.org/records/20412555 (DOI: 10.5281/zenodo.20412555). The processed numerical data underlying the graphs presented in the figures are also available on GitHub and Zenodo.

Funding: AF acknowledges support from the Molson Foundation (https://www.mcgill.ca/neuro/training/financial-support/studentships). BM acknowledges support from the Natural Sciences and Engineering Research Council of Canada (NSERC) (RGPIN-2017-04265) (https://nserc-crsng.canada.ca), Canadian Institutes of Health Research (CIHR) (PJT-180439) (https://cihr-irsc.gc.ca), Brain Canada Foundation Future Leaders Fund (https://braincanada.ca), the Canada Research Chairs Program (CRC-2022-00169) (https://www.chairs-chaires.gc.ca), the Michael J. Fox Foundation (MJFF-021133) (https://www.michaeljfox.org), and the Healthy Brains for Healthy Lives initiative (https://www.mcgill.ca/hbhl). The funders have no role in study design, data collection and analysis, decision to publish or preparation of the paper.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: ALK, alkaline phosphatase; ALT, alanine aminotransferase; AMICO, Accelerated Microstructure Imaging via Convex Optimization; AP, anterior-to-posterior; ASL, arterial spin labeling; AST, aspartate aminotransferase; ATT, arterial transit time; BMI, body mass index; DKT, Desikan-Killiany-Tourville; EPI, echo-planar imaging; FA, fractional anisotropy; FC, functional connectivity; FDR, false discovery rate; FFAs, free fatty acids; FLAIR, fluid-attenuated inversion-recovery; fMRI, functional MRI; FMRIB, Functional Magnetic Resonance Imaging of the Brain; FSH, follicle-stimulating hormone; GAMLSS, Generalized additive model for location, scale, and shape; GRE, gradient-recalled echo; HCP–A, Human Connectome Project–Aging; HDL, high-density lipoprotein; ICVF, intracellular volume fraction; IDPs, imaging-derived phenotypes; ISOVF, isotropic volume fraction; JHU, Johns Hopkins University; LDL, low-density lipoprotein; LH, luteinizing hormone; LV–I, first latent variable; LV–II, second latent variable; LVs, latent variables; MAP, mean arterial pressure; MB, multi-band; MD, mean diffusivity; MPRAGE, multi-echo magnetization-prepared rapid gradient echo; MRI, magnetic resonance imaging; NIMH, National Institute of Mental Health; NODDI, Neurite Orientation Dispersion and Density Imaging; OCD, obsessive-compulsive disorder; PA, posterior-to-anterior; pCASL, pseudo-continuous arterial spin labeling; PLS, partial least squares; RBC, red blood cell; SC, structural connectivity; SVD, singular value decomposition; TE, echo times; TI, inversion time; TIA, transient ischemic attack; TR, repetition time; WMH, white matter hyperintensity

Introduction

The human brain and body are highly interconnected throughout the life span [1,2]. Yet, the study of aging has typically treated cerebral and peripheral systems as separate entities. Currently, population-based aging trajectories are established for cortical thickness and gray matter density [37], brain volume and morphology [810], myelination [11,12], structural connectome [1315], functional connectome [1619], and cerebral blood perfusion [20,21]. Similarly, age-dependent trajectories are well-characterized for peripheral biomarkers, including body mass index (BMI), waist circumference, blood pressure, cholesterol, creatinine, albumin, bilirubin, glucose, glycosylated hemoglobin (HbA1c), high- and low-density lipoproteins (HDL and LDL), and endocrine measures such as testosterone and follicle-stimulating hormone [2229]. An emerging question is how these brain- and body-level measurements relate to each other.

Multi-modal neuroimaging is increasingly used to quantify the effects of typical aging and neurological disease on multiple tissue types and biological systems [30]. For instance, brain blood perfusion reduction and vascular dysregulation are linked with greater dementia risk, and can precede observable brain atrophy and clinical symptom onset of the disease by years [3136]. Nevertheless, routine clinical evaluation still relies more heavily on demographic information (age and sex) and laboratory-based assessments of blood and urine panels than on neuroimaging workup. Structural magnetic resonance imaging (MRI) (T1- and T2-weighted MRI) is used in occasional relevant scenarios—to rule out the possibility of focal neurological lesions such as primary or metastatic tumors or to indicate the presence of dominant atrophy—while more advanced MR imaging techniques such as functional MRI (fMRI), diffusion MRI, and arterial spin labeling (ASL) feature less prominently in clinical decision-making.

Recognizing the potential for peripheral biomarkers to serve as readily accessible indicators of brain health, there is greater effort to identify translatable brain–body relationships. Initial efforts have focused on isolating specific brain–body associations between individual features of interest. Notable examples include relationships between reduced glucose tolerance and hippocampal atrophy [37], between obesity and frontal cortex thinning and subcortical volume reduction [3840], and between hypertension and reductions in blood perfusion [41] and cortical thinning [42]. However, most of these studies focus on single brain measurements or a compact set of physiological markers. Without incorporating comprehensive measurements from both neural and peripheral systems, we cannot fully compare the sensitivity of brain features to particular physiological signatures.

Here we ask two questions. First, what can be inferred about brain health from individuals’ demographic and laboratory profiles? Second, among various MRI-derived brain measurements, spanning structural, functional, and vascular domains, which are most closely associated with specific physiological phenotypes? We address these questions using partial least squares (PLS) multivariate pattern learning to assess the covariance between multi-modal MRI brain measurements and a broad set of demographics and physiological characteristics [4345]. We analyze two datasets with comprehensive neuroimaging and peripheral multi-omics: the Human Connectome Project–Aging [4648] and UK Biobank [49]. We identify two generalizable axes of brain–body associations in both datasets and in both biological sexes (males and females): an aging axis and a metabolic axis. Furthermore, we identify brain features that contribute most to each axis. Finally, we examine how an individual’s position along these axes relates to their cognitive performance.

Results

The discovery dataset is obtained from the Human Connectome Project–Aging (HCP–A; https://www.humanconnectome.org/study/hcp-lifespan-aging). HCP–A data come from 597 participants (268 males; 329 females) aged 36–100 years [4648]. Detailed information on participants’ demographics, data acquisition, and preprocessing is provided in Methods.

We use partial least squares (PLS) [4345] to assess how participants’ age, blood pressure, body mass index (BMI), and plasma measurements (biomarkers; S1 Fig and S1 Table) covary with brain measurements derived from T1- and T2-weighted structural imaging, diffusion and functional magnetic resonance imaging, and arterial spin labeling (ASL) imaging. This multivariate analysis identified two statistically significant (assessed by permutation testing) and cross-validated latent variables (LVs) linking biomarkers to brain measurements in both males and females. In the following sections, we discuss these latent variables in detail. Throughout this report, we stratify the analysis by biological sex. There exist known differences between males and females in both brain and biomarker measures. For example, females typically exhibit higher cerebral blood perfusion than males [20,5058], along with distinct hormonal trajectories and notable differences in certain plasma markers (e.g., creatinine and lipid markers) [5963].

Finally, we use the UK Biobank dataset (https://www.ukbiobank.ac.uk) to replicate and validate the findings. UK Biobank data comprise 3,013 participants (1,431 males; 1,582 females) aged 51–83 years [49,64]. The biomarkers from this cohort are shown in S2 Fig and S2 Table.

We show biomarker intercorrelations for the HCP–A and UK Biobank cohorts in S3 and S4 Figs, respectively.

The aging axis

The first latent variable (LV–I) captures 66.74% and 71.90% of the covariance between biomarkers and brain measurements in males and females, respectively (, Nperm = 1,000 for both groups). LV–I is characterized by a biomarker profile composed of: greater age (the strongest contributor to LV–I), alongside higher levels of follicle-stimulating hormone (FSH), luteinizing hormone (LH), vitamin D, creatinine, urea, glycosylated hemoglobin (HbA1c), and mean arterial pressure (MAP) (Fig 1A). This biomarker profile is prominently associated with lower cortical thickness and longer cortical arterial transit time (Figs 1B and S5). Additional associations include lower fractional anisotropy (FA), cortical functional connectivity (FC) strength, and blood perfusion, and higher mean diffusivity (MD) and white matter hyperintensity (WMH). Cortical myelin content (quantified as T1/T2 ratio) and structural connectivity (SC) strength show relatively smaller contributions (Figs 1B and S5).

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Fig 1. Mapping biomarkers to brain features: first latent variable (LV–I) captures the aging axis.

Using PLS analysis, we identify a significant latent variable that accounts for 66.74% (males) and 71.90% (females) of the covariance between brain measurements and biomarkers—including demographics, BMI, blood pressure, and blood panel measurements. The PLS model includes 28 features on the biomarker side and 3,289 features on the brain side. (a) Biomarker loadings. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Each biomarker loading is divided by its bootstrap-estimated standard error, yielding a measure called “bootstrap ratio”. Bootstrap ratios are high for biomarkers with large weights (i.e., large contributions) and small standard errors (i.e., highly stable). Stable biomarkers for which the estimated 95% confidence intervals do not cross zero, are shown in red. (b) Brain loadings. Each dot represents a cortical brain region as defined by the Schaefer-400 parcellation [65] or a white matter tract defined by the JHU atlas [66,67]. For WMH, gray dots represent quantified WMH in cortical lobes and the total WMH burden. (c) Correlation between brain (x-axis) and biomarker scores (y-axis) for males (top; r = 0.75) and females (bottom; r = 0.70). Each dot represents an individual participant, colored by their age. The score per participant shows the extent to which the participant expresses the brain–biomarker association captured by LV–I. Score correlation values passed cross-validation in both sex groups.

https://doi.org/10.1371/journal.pbio.3003856.g001

Given that age is the strongest contributor to the LV–I pattern, we interpret LV–I as primarily capturing the “aging axis”. Other stable biomarker contributors align with age-related physiological changes (see S1 Fig). Blood urea and creatinine levels increase with age due to reduced glomerular filtration rate [6870]. FSH and LH increase with age in males [71] and in females as a result of age-related alterations in gonadal function [72] and in the hypothalamic-pituitary unit. HbA1c level increases with age independently of elevation in glucose level and insulin resistance [73]—partly as a result of age-related reduction in red blood cell (RBC) turnover and increased RBC lifetime; the prolonged RBC life span extends hemoglobin exposure to circulating glucose and enhances non-enzymatic glycation of hemoglobin, creating an age-dependent elevation in HbA1c [74]. MAP increases with age due to changes in peripheral vascular resistance and artery stiffness [75]. Fig 1C shows participants’ biomarker versus brain PLS scores, color-coded by participants’ age. In the PLS context, brain and biomarker scores quantify how strongly each participant expresses the brain–biomarker association captured by the latent variable loading profiles. Participants’ brain and biomarker scores along the LV–I dimension are correlated (r = 0.75 for males and r = 0.70 for females; , Nperm = 1,000 for both). The correspondence between brain and biomarker scores is cross-validated and is generalizable across participants in each biological sex group (, N = 100 for both groups).

Fig 2 shows the loading patterns for each brain measurement and the pairwise spatial similarity between these patterns along with the statistical significance of these similarities after accounting for spatial autocorrelation. In both biological sex groups, cortical thickness and cortical mean diffusivity (MD) loadings are negatively correlated; cortical MD and fractional anisotropy (FA) loadings are also negatively correlated. Together, these findings recapitulate the previously reported brain structural deterioration with age—. Notably, MD and ATT loadings are aligned, indicating that with age, brain regions with prolonged arterial transit time also have greater water diffusivity—. This coordinated pattern suggests that microstructural and vascular alterations in aging are interrelated.

The metabolic axis

The second latent variable (LV–II) captures 12.83% and 14.14% of the covariance between biomarkers and brain measurements in males and females, respectively (, Nperm = 1,000 for both). LV–II is characterized by a biomarker profile composed of: greater BMI, MAP, HbA1c, glucose, insulin, alanine aminotransferase (ALT), as well as lower high-density lipoprotein (HDL) (Fig 3A). On the brain side, this biomarker pattern is prominently associated with lower blood perfusion. Additional associations include lower FC strength and MD; the inverse association between BMI and MD potentially reflects the presence of gliosis [76]. Other cortical features make relatively smaller contributions (Figs 3B and S9).

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Fig 3. Mapping biomarkers to brain features: second latent variable (LV–II) captures the metabolic axis.

Using PLS analysis, we identify a second significant latent variable that accounts for 12.83% (males) and 14.14% (females) of the covariance between brain measurements and biomarkers—including demographics, BMI, blood pressure, and blood panel measurements. The PLS model includes 28 features on the biomarker side and 3,289 features on the brain side. (a) Biomarker loadings. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Each biomarker loading is divided by its bootstrap-estimated standard error, yielding a measure called “bootstrap ratio”. Bootstrap ratios are high for biomarkers with large weights (i.e., large contributions) and small standard errors (i.e., highly stable). Stable biomarkers for which the estimated 95% confidence intervals do not cross zero, are shown in red. (b) Brain loadings. Each dot represents a cortical brain region as defined by the Schaefer-400 parcellation [65], or a white matter tract defined by the JHU atlas [66,67]. For WMH, gray dots represent quantified WMH in cortical lobes and the total WMH burden. (c) Correlation between brain (x-axis) and biomarker scores (y-axis) for males and females (in both cases: r = 0.51). Each dot represents an individual participant, colored by their BMI. The score per participant shows the extent to which the participant expresses the brain–biomarker association captured by LV–II. Score correlation values passed cross-validation in both sex groups.

https://doi.org/10.1371/journal.pbio.3003856.g003

The LV–II biomarker pattern can be broadly interpreted as the “metabolic axis”. Biomarker contributors to this latent variable are highly interconnected. Excessive weight (high BMI) increases activity of sympathetic nervous system and renin-angiotensin-aldosterone system, leading to elevated blood pressure [7779]. High BMI is also linked to insulin resistance, a biological phenomenon where cells become less responsive to insulin for glucose transport [80]. Insulin resistance can be indexed by the homeostatic model assessment of insulin resistance (HOMA-IR), derived from fasting insulin and glucose concentration levels (their product divided by a constant) [81]. At the molecular level, insulin resistance develops through the accumulation of intracellular lipid metabolites, namely diacylglycerol and ceramide, which activate lipid-dependent serine/threonine kinase (including protein kinase C) and impair insulin signaling pathways through phosphorylation of insulin receptor substrates. Insulin resistance causes impaired insulin-mediated inhibition of lipolysis, leading to increased adipose tissue breakdown and elevated circulating free fatty acids (FFAs) that further inhibit the antilipolytic effect of insulin. Lipotoxic stress and elevated FFAs affect liver function and result in nonalcoholic fatty liver disease, elevated ALT, and systemic inflammation [82,83]. Hyperinsulinemia leads to chronic hyperglycemia and increases type 2 diabetes mellitus risk through progressive pancreatic -cell exhaustion [84]. Moreover, insulin resistance contributes to endothelial dysfunction and hypertension by impairing the PI3K/Akt pathway responsible for nitric oxide-mediated vasodilation while preserving the MAPK pathway that promotes vasoconstriction through endothelin-1 production. Elevated FFAs further contribute to vasoconstriction through direct effects on vascular smooth muscle cells [8587]. Hyperinsulinemia downregulates muscle lipoprotein lipase, reducing HDL generation from very-low-density lipoprotein processing and impairs insulin’s normal suppression of hepatic lipase, leading to increased breakdown of existing HDL particles and their rapid clearance from circulation [88]. Meanwhile, BMI has an inverse relationship with HDL; this relationship does not extend to low-density lipoprotein (LDL) and total cholesterol levels [89]. Fig 3C shows participants’ biomarker versus brain PLS scores, color-coded by participants’ BMI. Participants’ brain and biomarker scores along this latent dimension are correlated (r = 0.51 for both males and females). The correspondence between brain and biomarker scores is cross-validated and is generalizable in each biological sex group (, N = 100 for both groups).

Fig 4 shows the loading patterns for each brain measurement and the pairwise spatial similarity between these patterns along with the statistical significance of these similarities after accounting for spatial autocorrelation. In both biological sex groups, the blood perfusion and FC strength loadings are positively aligned, suggesting that metabolic-related reduction in perfusion is also reflected as reductions in FC strength of the same regions—. The third PLS latent variable did not pass cross-validation in either biological sex group (p = 0.16, 0.21 for males and females, respectively) and is therefore not described.

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Fig 4. LV–II brain loadings.

Lateral views of brain loadings for each included brain feature. Participants who more strongly express the biomarker pattern illustrated in Fig 3A (e.g., those with greater BMI) have lower blood perfusion. Brain maps are shown on the fsLR inflated cortical surfaces. Lateral and medial views of both hemispheres are shown in S10 Fig. The heatmaps show similarity of brain loadings across included brain measurements. Associations that remain significant after controlling for spatial autocorrelation (spin tests) and multiple comparison correction—using false discovery rate (FDR)—are marked with their corresponding correlation values (FC and blood perfusion: (males), pspin = 0.014 (females); FA and MD: (males), pspin = 0.014 (females); FA and SC: (males), pspin = 0.014 (females); myelin and SC: (males); thickness and myelin: (males); ATT and FC: (males); thickness and FA: pspin = 0.014 (females)). In S7B Fig, we reassess the significance of spatial similarity of the maps using the variogram-estimating null models. In S11 Fig, we compare the metabolic-axis brain loading patterns between males and females.

https://doi.org/10.1371/journal.pbio.3003856.g004

The metabolic axis is independent of age

We next assess whether the LV–II pattern, capturing the metabolic axis, is age-driven. To test this, we regress out the non-linear effect of age from all features included in the PLS model (biomarkers and brain measurements) using generalized additive models for location, scale, and shape (GAMLSS) [90]. We then rebuild the PLS model using age-corrected features. In this updated model, LV–I captures 34.91% and 46.15% of the covariance between age-corrected biomarkers and age-corrected brain measurements in males and females, respectively (, Nperm = 1,000 for both). The LV–I pattern is shown in Fig 5 and it resembles LV–II from the original PLS model (based on uncorrected data; Fig 3), albeit with some differences (e.g., in males, vitamin D becomes a stable contributor; in females, vitamin D is no longer stable, while calcium becomes stable). This latent variable is cross-validated in both sex groups (, N = 100 for both groups).

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Fig 5. Mapping biomarkers to brain features after regressing out the age effect: first latent variable (LV–I) captures the metabolic axis.

We use GAMLSS models to regress out the age effect from all included features prior to the implementation of the PLS model (age is regressed out from both brain and biomarker measures). We identify a significant latent variable that accounts for 34.91% and 46.15% of the covariance in the data for males and females, respectively. The PLS model includes 28 features on the biomarker side and 3,289 features on the brain side. (a) Biomarker loadings. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Each biomarker loading is divided by its bootstrap-estimated standard error, yielding a measure called “bootstrap ratio”. Bootstrap ratio is high for biomarkers with large weights (i.e., large contributions) and small standard errors (i.e., highly stable). Stable biomarkers for which the estimated 95% confidence intervals do not cross zero, are shown in red. (b) Brain loadings. Each dot represents a cortical brain region as defined by the Schaefer-400 parcellation [65], or a white matter tract defined by the JHU atlas [66,67]. For WMH, gray dots represent quantified WMH in cortical lobes and the total WMH burden. See S12 Fig for brain loadings shown on the fsLR cortical surface. (c) Correlation between brain (x-axis) and biomarker scores (y-axis) for males (top; r = 0.52) and females (bottom; r = 0.51). Each dot represents an individual participant, colored by their BMI. The score per participant shows the extent to which the participant expresses the brain–biomarker association captured by LV–I.

https://doi.org/10.1371/journal.pbio.3003856.g005

This first latent variable highlights the link between poor body metabolic profile (characterized by higher BMI, MAP, HbA1c, glucose, insulin, and ALT, and lower HDL) and lower brain blood perfusion. The spatial pattern of reduction in blood perfusion aligns with the FC strength reduction pattern (S12 Fig). Given that the most extreme stable biomarker loadings are similar across males and females, we further assess the similarity of brain loadings across sexes. We find the highest correspondence for ATT (r = 0.82, FDR-corrected , ) and blood perfusion maps (r = 0.63, FDR-corrected , ), respectively. Structural connectome strength (r = 0.06, FDR-corrected pspin >0.05, pSMASH > 0.05), FA (r = 0.20, FDR-corrected , ), and myelin maps (r = 0.26, FDR-corrected , ) exhibit lower cross-sex spatial correspondence (S13 Fig). In S14 Fig we show the superiority of blood perfusion measure over other functional and structural brain imaging measurements in capturing the potential effects of worse metabolic index. Taken together, these findings indicate that the captured metabolic axis reflects a robust pattern beyond age-related variations. Rather, it reflects a distinct link between systemic metabolic dysfunction and vascular and functional alterations in the brain.

Cognitive relevance of aging and metabolic dysfunction

What are the behavioral manifestations of the captured brain–body interaction axes in the typical aging cohort? The HCP–A dataset provides a rich array of neuroimaging, demographic, physiological, and cognitive assessments that allow us to address this question. Here, we examine the link between a range of cognitive measures (fluid, crystallized, and total cognition composite scores) and participants’ brain scores on the “aging” and “metabolic” axes.

Participants (both males and females) with greater expression of brain patterns shown in Figs 1B and 2 (LV–I brain pattern; greater age) have lower cognitive flexibility and total cognition scores. Meanwhile, they perform better on crystallized cognition tasks, indicating stronger performance in abilities heavily influenced by prior learning (Fig 6A). Female participants with greater expression of multivariate brain patterns shown in Figs 5B and S12—characterized by metabolic dysfunction—also express cognitive differences compared to their more metabolically healthy female counterparts and perform worse in tasks requiring cognitive flexibility (Fig 6B). This finding aligns with reported sex differences in the association between metabolic syndrome and dementia, with metabolic syndrome being significantly associated with cognitive impairment in women only [9196]. In short, fundamental physiological and neuroimaging indicators of metabolic status manifest in individual differences in cognitive performance.

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Fig 6. Cognitive relevance of aging and metabolic axes.

(a) Spearman’s rank correlation between LV–I brain scores and total, fluid, and crystallized cognition composite scores (total cognition: , (males), , (females); fluid cognition: , (males), , (females); crystallized cognition: , (males), , (females)). (b) Spearman’s rank correlation between LV–I brain score and cognitive measures, while GAMLSS models are used to correct for non-linear age effects across the cognitive variables. In this case, LV–I is capturing the metabolic axis (see Fig 5). Total and fluid cognition composite scores are negatively associated with brain scores in females (total cognition: , (females); fluid cognition: , (females)). Reported p-values are corrected for multiple comparisons using FDR within each biological sex group.

https://doi.org/10.1371/journal.pbio.3003856.g006

Replication: aging and metabolic axes in UK Biobank

To replicate the findings, we use the UK Biobank dataset (https://www.ukbiobank.ac.uk; see Methods). We use PLS to assess how plasma and urine panel measures, age, blood pressure, BMI, and various anthropometric measurements (hip, waist, and body fat percentage) covary with a series of brain measures (see S2 Fig) [97]. The assessed brain measurements include ASL-derived ATT and blood perfusion, cortical thickness, area and volume of brain regions in addition to FA, MD, intracellular volume fraction (ICVF), isotropic volume fraction (ISOVF) of white matter tracts, and quantified whole-brain white matter hyperintensity (WMH) volume. Imaging acquisition parameters, parcellations (Desikan-Killiany atlas for cortex), and preprocessing pipelines for the UK Biobank dataset are all different from those used in the HCP–A dataset. In the following paragraphs, we discuss the first two statistically significant and cross-validated LVs for both males and females.

The first latent variable captures 75.71% and 78.11% of the covariance between biomarkers and brain measurements in males and females, respectively (, Nperm = 1,000 for both). The biomarker profile for LV–I is prominently driven by age (S15A Fig), indicating that aging is associated with longer ATT, higher WMH volume, lower blood perfusion, lower cortical and subcortical volumes, lower cortical areas and thickness, in addition to lower white matter FA, lower ICVF, higher white matter MD, and higher ISOVF (S15B and S16 Figs). This pattern is similar to the “aging axis” presented in Fig 1. The directionality of microstructural changes found here is aligned with age-associations in the UK Biobank dataset previously described by Cox et al. [98].

The second latent variable captures 15.33% and 14.93% of the covariance between biomarkers and brain measurements in males and females, respectively (, Nperm = 1,000 for both). The biomarker profile for LV–II captures the metabolic dysfunction profile (S17A Fig). LV–II biomarker profile highlights low HDL and age, along with high BMI, hip and waist circumferences, body fat percentage, diastolic blood pressure, ALT, aspartate aminotransferase (AST), triglycerides, C-reactive protein—previously linked to metabolic syndrome and inflammatory disorders [99]—and sodium in urine. This metabolic profile is dominantly associated with lower brain blood perfusion (S17B and S18 Figs).

We further show that the LV–II (metabolic axis) from UK Biobank is not age-driven. We use GAMLSS models to regress out the non-linear age effects (as well as the site effect) from all biomarkers and brain features; we then rebuild the PLS model. S19 Fig shows the first latent variable (LV–I), which again resembles the biomarker profile associated with metabolic dysfunction and highlights its relevance to blood perfusion (also see S20 Fig). Last, we examine how brain scores from LV–I (after correcting for age) relate to participants’ fluid intelligence. In both female and male groups from the UK Biobank dataset, poorer metabolic health is associated with lower fluid intelligence scores (, (males), , (females)) (S21 Fig).

Validation and sensitivity analysis

We next ask whether a PLS model trained on one dataset (HCP–A) explains brain–biomarker relationships in an independent cohort (UK Biobank). To answer this question, we first identify the brain features and biomarkers shared across the two datasets. Shared brain features include white matter FA, white matter MD, WMH, blood perfusion, ATT, and cortical thickness. Shared biomarkers include age, BMI, ALK, AST, ALT, urea, calcium, creatinine, bilirubin, glucose, HbA1c, HDL cholesterol, LDL cholesterol, triglycerides, total cholesterol, testosterone, total protein, and vitamin D. For each individual, brain features are averaged across all available parcels, yielding six global brain measures per individual. Using these shared features (6 brain measures and 18 biomarkers), we construct sex-stratified PLS models exclusively in the HCP–A dataset. Again, in both males and females, the first latent variable (LV–I) predominantly captures age-related covariations and the second latent variable (LV–II) captures metabolic-related covariations (S22 Fig).

In males, LV–I indicates that greater age is associated with lower cortical thickness, FA, and blood perfusion, greater MD and WMH load, and longer ATT (brain and biomarker score correlation r = 0.68, , Nperm = 1,000). LV–II indicates that worse metabolic function is associated with lower blood perfusion and shorter ATT (brain and biomarker score correlation r = 0.43, , Nperm = 1,000). Next, we project the UK Biobank brain and biomarker data onto the HCP–A-derived PLS weight vectors. We find a significant correlation between projected brain and biomarker scores in the UK Biobank cohort. We assess the significance of the correlation value by permuting the order of UK Biobank subjects on the biomarker side (Nperm = 10,000), while keeping brain data fixed, and constructing a null distribution of correlations from the projected data. For LV–I, the Pearson correlation between projected brain and biomarker scores in UK Biobank is equal to 0.41 (). For LV–II, the Pearson correlation between projected brain and biomarker scores in UK Biobank is equal to 0.12 ().

In females, LV–I indicates that greater age is associated with lower cortical thickness, FA, and blood perfusion, greater MD, and WMH load (brain and biomarker score correlation r = 0.68, , Nperm = 1,000). LV–II indicates that worse metabolic function is associated with lower blood perfusion, lower MD, and shorter ATT (brain and biomarker score correlation r = 0.36, , Nperm = 1,000). Next, we project the UK Biobank data into the HCP–A-derived PLS space. For LV–I, the Pearson correlation between projected brain and biomarker scores in UK Biobank is equal to 0.46 (). For LV–II, the Pearson correlation between projected brain and biomarker scores in UK Biobank is equal to 0.13 (). Together, these results demonstrate that the brain–biomarker covariance structure identified in HCP–A—including both the age-dominated and metabolic latent variables—shows correspondence in an independent dataset. Notably, when the model developed on the HCP–A data is used to explain the associations in the UK Biobank data, the resulting score correlation values are modest relative to the discovery sample, which may reflect differences in age range and imaging granularity across datasets.

We also assess the potential instability of PLS results arising from the high dimensionality of the brain feature space relative to sample size [100]. To this end, each brain feature is averaged across all parcels, yielding a single global value per brain measure per participant and substantially reducing the PLS input dimensionality. Rebuilding the PLS models using this reduced feature set yields latent variables that are highly consistent with those obtained from the original analysis. Across both biological sexes and both datasets (HCP–A and UK Biobank), LV–I captures brain–body covariation related to aging and LV–II captures covariation related to metabolic dysfunction, confirming that the main findings are not artifacts of the high dimensionality of the PLS model input.

In the HCP–A dataset, LV–I indicates that greater age is associated with low cortical thickness, myelin, FA, functional and structural connectivity strength, and blood perfusion, alongside high MD, WMH load, and ATT (score correlation: males = 0.72, females = 0.68; variance explained: 82.87% and 83.89%, respectively; for both) (S23 Fig). LV–II is characterized by lower HDL, higher BMI, MAP, insulin, and HbA1c, and worse liver enzyme profiles on the biomarker side, and is associated with low blood perfusion and MD on the brain side (score correlation: males = 0.48, females = 0.50; variance explained: 10.29% and 10.79%, respectively; for both) (S24 Fig).

In the UK Biobank dataset, LV–I indicates that greater age is associated with low cortical thickness, volume, FA, ICVF, and cortical area, alongside high MD, ISOVF, WMH load, and ATT (score correlation: males = 0.60, females = 0.57; variance explained: 84.16% and 87.21%, respectively; for both) (S25 Fig). LV–II is characterized by higher BMI, body fat percentage, waist and hip circumference, and worse liver enzyme profiles on the biomarker side, and is associated with low blood perfusion and MD on the brain side (score correlation: males = 0.27, females = 0.24; variance explained: 11.12% and 9.10%, respectively; for both) (S26 Fig).

The correspondence between biomarker and brain scores is cross-validated and is generalizable across participants in each biological sex group and both datasets (, N = 100).

Discussion

In the present report, we analyze data of HCP–Aging and UK Biobank cohorts to characterize the multivariate relationships between a series of brain measurements and bodily physiological phenomics—including age, body mass index (BMI), blood pressure, and plasma/urine protein profiles [4649,64]. The PLS analysis [4345] reveals two principal axes of brain–body associations: one driven primarily by age, and the other by metabolic health. The most prominent axis of association is age-related. In both datasets, increased age is associated with cortical thinning and microstructural alteration, along with longer arterial transit time and reduced cerebral blood perfusion. The second axis of brain–body covariance is related to metabolic features. Elevated BMI, blood pressure, HbA1c, glucose, and ALT liver enzyme, along with lower HDL cholesterol are linked to lower brain blood perfusion. We further show that the captured metabolic effect on the brain is accompanied by lower cognitive flexibility, reflecting the potential behavioral consequences of the observed brain–body relationships.

Aging is a time-dependent biological phenomenon that affects every system in the human body [101], from the skeletal and muscular to the cardiovascular and nervous systems. Previous research on brain aging has established typical aging trajectories for various neuroimaging measures that serve as benchmarks to detect pathological deviations from the norm [18]. Age-related brain changes are now documented across multiple brain features, including cortical thickness [3,5,6,102105], gyrification [104], brain tissue volume [13,18,106], FA [107111], MD [13,109,110,112,113], SC [14,114,115], FC [17,19,114,116119], and blood perfusion [20,21,58]. Across these modalities, there is growing consensus regarding age-related structural deterioration and reorganization of brain vascular and functional networks.

PLS brain loadings for the aging axis show consistent directionality in both datasets, reflecting brain structural deterioration alongside cerebrovascular decline. Specifically, we recapitulate age-related structural deterioration, characterized by , as well as cerebrovascular dysfunction, characterized by . However, while cortical thickness shows the greatest loading magnitude (e.g., most affected by aging) in HCP–Aging, blood perfusion, transit time, and white matter hyperintensity loadings dominate in UK Biobank. The differences in brain loading ranking may originate from distinct age ranges in HCP–Aging (36–100 years) and UK Biobank (51–83 years) cohorts, or from their imaging protocol differences.

Our study resonates with a growing appreciation for studying brain aging from a wider, multivariate perspective, and is in line with the studies that suggest superior brain-age prediction accuracy when incorporating multi-modal brain imaging—T1-weighted MRI, T2-FLAIR, T2*, diffusion-MRI, task- and resting-state fMRI—compared to single-modality approaches [120124]. Our findings emphasize that the spatial patterns of age-related changes are not identical across “all” brain features. For example, while FA and MD have spatially similar age-related profiles, blood perfusion exhibited a distinct pattern of age-related decline; suggesting that different neuroimaging measures capture complementary aspects of brain aging. We further show that age-related brain loadings are relatively consistent across biological sex groups.

One consistent and reproducible finding across this study is the identification of a metabolic axis linking peripheral physiological markers and the brain. Prior studies have shown that metabolic factors are associated with brain health; for example, increased BMI and abdominal fat have been linked to both functional [125] and structural brain alterations [38,39,126136]; and increased HbA1c and adiposity-related insulin resistance are linked to cortical thickness changes [137,138]. Extending beyond these previously documented associations, we show that cerebral blood perfusion is the primary brain feature that potentially declines as a function of elevated metabolic risk factors. One possibility is that vascular susceptibility to metabolic risks constitutes the principal biological mechanism underlying the brain–body metabolic axis in aging populations. Elevated LDL cholesterol [139141], glucose, glycosylated hemoglobin [142], blood pressure [143145], body fat and possibly BMI [146], as well as low HDL cholesterol [147] increase atherosclerotic and cardiovascular disease risk, compromise vascular integrity, and ultimately impair perfusion.

Various biological pathways have been suggested to explain how metabolic abnormalities may disrupt endothelial function. For instance, HDL is known to have anti-inflammatory and antioxidant properties [148], by mediating cholesterol trafficking and reducing oxidized lipids from LDL, inhibiting endothelial apoptosis and stimulating their migration, and preventing monocyte adhesion to the endothelial surface—a critical step in the development of atherosclerotic plaques [149151]. When HDL levels are low, vascular resilience is reduced, leaving the brain particularly vulnerable to vascular injury. Indeed, low serum HDL is linked to compromised blood-brain barrier integrity, increased cerebral amyloid burden [152] and enhanced -amyloid accumulation within cerebral vessels [153]; there are also studies that report association of lower HDL (and ApoAI, the major protein component of HDL) with Alzheimer’s disease and individual cognitive performance [153158]. Taken together, a healthier metabolism may foster vascular resilience and vascular reactivity and sustain healthy cerebral blood perfusion, which further protects against neurodegeneration.

The perfusion-centric metabolic effect can partly explain the disparate structural effects of metabolic risk factors reported to date [159]. While most studies report reductions in frontal cortex volume and thickness in obesity [39,127,128,130,132134,136], some report overall gray matter loss or even white and gray matter expansion [40,135,160]. In our PLS model, the metabolic axis is characterized by lower frontal cortex thickness and greater occipital cortex thickness in the HCP–A dataset. This pattern is consistent with independent findings [128,135,161,162] and is in line with the findings of Petersen and colleagues [163], who reported a similar cortical thickness pattern associated with metabolic syndrome risk factors when analyzing data of over 40,000 UK Biobank participants. Several mechanisms are proposed for obesity- and metabolic syndrome-related cortical thickening in occipital cortex, ranging from neuroinflammation [162] to enhancement of visual processing and attention networks in obesity [135]. Given that metabolic markers covary most strongly with cerebral blood perfusion in both datasets, future neuroimaging studies of obesity and metabolic syndrome may achieve greater consistency by including blood perfusion measures when assessing brain health.

Our results also suggest a pattern of blood plasma markers and body vitals that are closely associated with brain physiology. Defining “metabolic dysfunction” remains an important challenge in the field, with ongoing debate over which features should be included in clinical definitions [164167]. Current discussions often focus on including or excluding features from the definition, often without a specific weighting of the relative importance of these plasma and urine factors in the neurologic context. For instance, one definition of metabolic dysfunction is presence of three or more of the listed elements including elevated glucose, blood pressure, triglycerides, waist circumference, and reduced HDL [168]. Our cross-dataset and cross-sex consensus suggests that higher HDL cholesterol may be neuroprotective, while elevated BMI, HbA1c, blood pressure, and ALT consistently emerge as factors associated with lower brain blood perfusion.

This study provides a framework for studying the mechanisms of neuroprotection and vulnerability in metabolic dysfunction. Not all individuals exposed to metabolic dysfunction experience equivalent brain outcomes. Some individuals demonstrate resilience to expected metabolic brain correlates despite peripheral risk factors, while some show heightened vulnerability (discrepancy between brain and peripheral biomarker profiles; see S27 Fig). While part of this discrepancy may originate from measurement errors, it is also conceivable that genetic predisposition and environmental factors modulate the heterogeneity of interactions between brain and peripheral features [169]. Our framework quantifies this discrepancy and provides an opportunity for targeted genetic investigations to identify genetic variants that may confer resilience to brain alterations caused by metabolic risks [170] and to test the contribution of behavioral and lifestyle factors—such as smoking, physical activity, socioeconomic status, and pollution exposure—on shaping this discrepancy. One plausible example of how genetics can alter the association between brain and bodily metabolic signature is detailed here: vascular dysfunction and arterial stiffness partially mediate the link between systemic metabolic conditions and brain blood flow, function and structure [171], meanwhile, specific genes are known to contribute to individuals’ propensity to develop arterial stiffening [172,173], which may, in turn, amplify the downstream effects of metabolic abnormalities on the brains of these vulnerable individuals. It is important to note that in the present report resilience and vulnerability are defined with respect to normative brain–body associations estimated across the full cohort. These cross-sectional findings should therefore be replicated in longitudinal studies to assess individual vulnerability and resilience over time.

The brain–body metabolic axis may in part reflect background genetic predisposition rather than a direct causal effect of peripheral metabolic dysfunction on the brain. Most obesity-associated genes are expressed in the central nervous system, with obesity-associated loci overlapping with genes and pathways implicated in neurodevelopment [174,175]. These genetic influences extend beyond energy homeostasis and reward-related brain areas, and affect broadly distributed neural circuits across the brain [176]. In other words, rather than the presence of a pure “causal” relationship between metabolic dysfunction and brain features, it is possible that individuals with higher genetic risk for obesity also have genetic propensity for the brain patterns identified in this study [135]. In line with this notion, Morys and colleagues have shown that polygenic risk scores for obesity are negatively correlated with frontal cortex thickness and volume in adolescents (ABCD cohort; mean age = 10 years) [177]. This brain pattern is related to increased impulsivity and subsequent BMI increase at one-year follow-up [178]. Hence, genetic predisposition may initiate chronic obesity and cardiovascular consequences that further impact the brain in older individuals. In either case, reversible brain alterations (both functional and structural) following weight loss [179184] highlight the contribution of modifiable lifestyle factors in maintaining brain health. Indeed, weight loss, following either Roux-en-Y gastric bypass surgery [185] or a simple 12-month behavioral change (diet and exercise) has been shown to increase cerebral blood flow [186].

Lifestyle changes that ameliorate (or avoid) metabolic dysfunction can have a significant clinical relevance due to their influence on brain blood perfusion health. Hypoperfusion and vascular dysfunction impair the brain’s clearance of solutes and metabolites through compromised interstitial fluid drainage leading to accumulation of toxic proteins [187,188]. Simultaneously, hypoperfusion induces oxidative stress, promoting the formation of misfolded proteins and amyloid- () precursors, and further reducing the expression and activity of neprilysin, a major -degrading enzyme [189]. These pathological processes create a vicious cycle, as peptides themselves can further impair vasoregulation [190] and reduce blood flow [191], perpetuating the hypoperfusion that initially contributed to their formation. Meanwhile, animal studies have shown that induced hypoperfusion can accelerate cerebral amyloid angiopathy [192]. In short, a potential mechanistic explanation is that obesity leads to cerebrovascular alterations, which in turn facilitates amyloid- deposition in brain tissue (leading to Alzheimer’s disease) and amyloid formation in brain vasculature system (leading to cerebral amyloid angiopathy). Furthermore, reduced blood flow due to arterial narrowing promotes thrombosis and increases risk of emboli formation [193]. Maintaining metabolic health may thus prevent or slow down neurodegenerative cascades by preserving brain perfusion.

The present study is part of a wider effort to understand links between the brain and the body. These bidirectional interactions are increasingly explored in the context of the gut-brain axis [194] and the proteomics-brain axis [195,196]. The gut-brain axis consists of two communication mechanisms: one mediated by chemicals including neurotransmitters, neuropeptides, hormones, and gut microbiome [197], and the other mediated by the physical connections via the vagus nerve. There is evidence that this axis of interaction plays a role in obesity and metabolic health via serotonergic signaling [198,199]. Concurrently, proteomics can also help to monitor brain health by defining protein signatures associated with obesity and type 2 diabetes. The identified protein profiles enable the identification of potential target molecules for effective intervention plans [195,196,200203].

Importantly, both aging and metabolic brain signatures have behavioral relevance across participants. We replicate well-known associations between aging and cognitive domains; in particular, we find the relationship between aging and diminished cognitive flexibility [204207]. In addition, participants with greater scores on the metabolic dysfunction axis show greater cognitive impairment compared to their metabolically healthier counterparts. This finding aligns with reports documenting the interplay between diabetes mellitus type 2, low cerebral blood flow and worse memory, executive function and processing speed [208], as well as studies linking cortical thickness or brain structural volume signatures of BMI and metabolic status to participants’ working memory performance [209], fluid intelligence and prospective memory [210]. Note, however, that there are several studies that find no significant associations between specific metabolic syndrome features and cognition [211,212]. The present report shows that a composite metabolic brain–body profile can identify links between physiological measurements and cognitive outcomes.

Our results point to possible sex differences in metabolic-cognitive associations. In the HCP–A dataset, greater metabolic deviation from health is associated with lower fluid cognition scores in females, whereas no significant negative associations survive multiple comparison correction in males. Consistent with prior reports [131,213216], we also find that metabolic burden affects brain structure and function differently in males and females (e.g., as reflected by partial divergence in brain loadings; see S11 and S13 Figs). Greater female cognitive susceptibility to metabolic dysregulation is also reported in multiple independent studies [9196]. The potentially greater cognitive effects observed in females may account for the higher Alzheimer’s disease prevalence in females compared to males [217]. Differential cognitive risk and resilience may be driven by sex-related factors ranging from physiological differences to acquired socioeconomic disparities [218,219]. For example, sex hormones may influence blood-brain barrier integrity, endothelial function, and vascular regulation [220223]—systems that are also sensitive to metabolic dysfunction—thereby shaping sex-specific vulnerability to metabolic brain injury. Metabolic health and sex differences should be integrated in future aging and neurodegenerative disease studies to understand cognitive resilience disparities across individuals in greater detail.

The present findings should be interpreted with respect to several methodological considerations. First, cross-sectional associations between brain measurements and peripheral biomarkers are not causal—longitudinal studies, and interventional studies—e.g., brain imaging before and after obesity-reduction trials—can help understand the nature of associations (causal or co-existence). Second, while our findings suggest that ASL imaging may offer greater sensitivity for obesity and metabolism research, the inherently low signal-to-noise ratio of this imaging modality and its sensitivity to obesity-related confounds (such as motion artifacts, different body composition, and head placement [224226]) is an ongoing topic of research. Encouragingly, changes in FC strength and in perfusion in the presence of metabolic dysfunction are similar. Third, in the UK Biobank dataset, laboratory-based biomarkers were acquired at the baseline visit, whereas the neuroimaging data were acquired during a follow-up session (time interval between sessions can span several years, see S2 Fig). We addressed this temporal discrepancy by using GAMLSS models to regress out age effects from all features entered into the PLS analysis. Fourth, the present statistical model is sensitive only to linear relationships between brain and body features [43], and does not consider the possibility that multiple such relationships are non-linear. In other words, the latent axes identified in this study do not characterize the full picture of the underlying brain–body associations which may have a complex non-linear nature. As comprehensively phenotyped datasets become larger, it may be possible to fit more complete and complex models that additionally encode non-linear relationships between brain features and systemic biomarkers. Last, many of the biomarkers included in this study are directly linked to the metabolic status of the body and are highly interconnected (e.g., HDL, LDL, BMI, total cholesterol). Indeed, the choice of biomarkers shapes the reported axes of brain–body covariance in this report and contributes to the prominence of the metabolic latent variable. Future work incorporating more diverse and comprehensive plasma and urine measures may reveal latent brain–body dimensions that extend beyond the metabolic axis.

Materials and methods

All code used to perform the analyses is available on GitHub at https://github.com/netneurolab/Farahani_Age_Metabolism and has been archived and on Zenodo at https://zenodo.org/records/20412555 (https://doi.org/10.5281/zenodo.20412555).

HCP–A: Demographics

We analyzed data from 597 participants (268 males; 329 females) aged 36–100 years from the HCP–Aging dataset (HCP Lifespan studies, 2.0 Release) [4648]. Participants represented a “typical” aging population and had common health conditions (e.g., hypertension) without identified pathological causes of cognitive decline (e.g., stroke). All HCP participants gave written informed consent prior to data collection. All study procedures were conducted in accordance with the principles expressed in the Declaration of Helsinki and were approved by the Institutional Review Board at Washington University in St. Louis (IRB ID: 201,603,117). The HCP-Aging data was accessed through the National Institute of Mental Health (NIMH) Data Archive under an approved Data Access Request/Data Use Certification, DAR ID: 20,074.

HCP–A: Brain imaging acquisition

All HCP–A brain imaging data were acquired using a 3.0 Tesla Prisma scanner (Siemens; Erlangen, Germany) and a 32–channel Prisma head coil [4648].

T1-weighted structural data were acquired using a multi-echo magnetization-prepared rapid gradient echo (MPRAGE) sequence with the following parameters: repetition time (TR) =2,500 ms, inversion time (TI) =1,000 ms, echo times (TE) =1.8/3.6/5.4/7.2 ms, spatial resolution mm3, number of echoes = 4, and flip angle . T2-weighted structural data were acquired using a 3D sampling perfection with application-optimized contrasts using different flip angle evolutions (SPACE) sequence, with the same spatial resolution as the T1-weighted image. Parameters for the T2-weighted sequence were: TR = 3,200 ms, TE = 564 ms, and turbo factor = 314. Both T1- and T2-weighted images captured a sagittal field of view measuring mm and a matrix size of slices. Additional acquisition parameters included 7.7% slice oversampling, 2-fold in-plane acceleration (GRAPPA) in the phase encoding direction, and a 744 Hz/Px pixel bandwidth. T1- and T2-weighted structural data provided the anatomical reference for analysis of all imaging modalities, reconstruction of cortical surfaces, and estimation of cortical myelin content (T1/T2 ratio) and cortical thickness [46].

Diffusion data were acquired using a spin-echo echo-planar imaging (EPI) sequence with the following parameters: TR = 3.23 s, flip angle , spatial resolution mm3, 185 directions on 2 shells, b = 1500/3000 s/mm2, along with 28 b = 0 s/mm2 images. These data were used to derive FA, MD, and structural connectome strength metrics.

Resting-state fMRI data with blood-oxygen-level-dependent (BOLD) contrast were acquired using a 2D multi-band gradient-recalled echo (GRE) echo-planar imaging (EPI) with the following parameters: TR/TE = 800/37 ms, flip angle , and spatial resolution mm3. Functional scans were acquired in pairs of two runs (four runs in total per participant, each run lasting 6.5 min), with opposite phase encoding polarity so that the fMRI data in aggregate were not biased toward a particular phase encoding polarity (two runs with anterior-to-posterior (AP) phase encoding and two runs with posterior-to-anterior (PA) phase encoding). During the fMRI scan, participants viewed a small white fixation crosshair on a black background. The functional MRI minimal preprocessing steps that were applied to the data are provided by Glasser and colleagues [227].

Blood perfusion and arterial transit time were measured using arterial spin labeling (ASL) magnetic resonance imaging (MRI) [58,228]. ASL data were acquired using a pseudo-continuous arterial spin labeling (pCASL) and 2D multi-band (MB) echo-planar imaging (EPI) sequence. Pseudo-continuous ASL data were acquired with a labeling duration of 1,500 ms and five post-labeling delays of 200 ms, 700 ms, 1,200 ms, 1,700 ms, and 2,200 ms, containing 6, 6, 6, 10, and 15 control-label image pairs, respectively. To calibrate perfusion measurements into units of ml/100g/min, two PD–weighted M0 calibration images (TR > 8 s) were acquired at the end of the pCASL scan. Other sequence parameters included spatial resolution mm3 and TR/TE = 3,580/18.7 ms. For susceptibility distortion correction, two phase-encoding-reversed spin-echo images were also acquired. During the ASL scan, participants viewed a small white fixation crosshair on a black background (5.5 min). The ASL data preprocessing was conducted following the ASL Pipeline for the Human Connectome Project available at https://github.com/physimals/HCP-asl (explained in detail in Kirk and colleagues [228]). To run this preprocessing pipeline, we used the QuNex platform (singularity container, version 0.99.1) [229].

HCP–A: Brain imaging measurements

To link neuroimaging measurements with peripheral biomarkers, we incorporated a comprehensive set of cortical and subcortical features. For cortex, the following measures were included: cortical thickness, myelin, fractional anisotropy (FA), mean diffusivity (MD), cerebral blood perfusion, arterial transit time (ATT), functional connectivity (FC) strength, and structural connectivity (SC) strength. All cortical measures were parcellated using the Schaefer-400 atlas [65].

For white matter, we used the Johns Hopkins University (JHU, threshold 25%) atlas to extract FA, MD, blood perfusion, and arterial transit time across 20 white matter tracts [66,67]. White matter hyperintensities (WMH) were represented by nine measures, one reflecting the total WMH voxel count and eight reflecting WMH voxel counts within each cortical lobe (frontal, temporal, parietal, and occipital), separately for the left and right hemispheres.

Altogether, the brain feature set included 3,289 values. Among the 597 participants included in the multivariate mapping between brain and biomarkers, 63 males and 62 females had missing values for WMH measurements. All missing values were imputed using the median of the corresponding sex-specific feature.

HCP–A: Biological samples and vital signs

The HCP–A dataset included a comprehensive array of participant-specific blood biochemistry results and physiological measurements [48]. These assessments included common health indicators including total protein, glucose, insulin, glycosylated hemoglobin (HbA1c), triglycerides, low-density lipoprotein (LDL), high-density lipoprotein (HDL), total cholesterol, albumin, bilirubin, creatinine, urea, chloride, sodium, potassium, calcium, vitamin D, and CO2 content, as well as liver metabolic enzymes including alanine aminotransferase (ALT), aspartate aminotransferase (AST), and alkaline phosphatase (ALK). Multiple hormonal measures were also obtained, including serum estradiol, testosterone, luteinizing hormone (LH), and follicle-stimulating hormone (FSH). Blood samples were collected, preferably after an 8–h fasting period. Furthermore, participants’ height and weight were also recorded, allowing the calculation of body mass index (BMI). Systolic and diastolic blood pressure/pulse values were measured, from which the mean arterial pressure (MAP) was derived. Participants’ age was also provided. In total, 28 biomarkers were included in the analysis for each participant.

Among the 597 participants (268 males; 329 females) with available biochemical data, some had missing values for specific measures: 2 females for BMI, 2 males and 4 females for MAP, 1 male and 3 females for HbA1c, 2 males and 1 female for FSH, 2 males and 1 female for LH, 2 males and 1 female for Estradiol, and 1 male and 1 female for Testosterone (see S1 Table). In these instances, the missing values were imputed using the median of the respective measure (within each sex group) to prevent not-a-number values in the PLS analysis.

HCP–A: Cognitive assessment

Cognitive performance in HCP–A participants was evaluated using the NIH Toolbox for the Assessment of Neurological and Behavioral Function (NIH-TB). Crystallized, fluid, and total cognitive composite scores were obtained for all participants. Crystallized cognitive composite score captured abilities influenced by acquired knowledge and was derived from two assessments: the oral reading recognition test and the picture vocabulary test. Fluid cognition composite score captured processing efficiency and novel problem-solving abilities. This composite score was derived from five components, including dimensional change card sort test, list sorting working memory test, picture sequence memory test, pattern comparison processing speed test, and flanker inhibitory control and attention test. In this study, composite scores were used in place of individual test scores due to their enhanced reliability and reduced measurement error [230].

When calculating correlations between PLS scores and cognitive scores, data from individuals with missing cognitive scores were excluded. Among females, 36 missing values existed for cognitive measures, and among males 54 missing values existed for crystallized and total cognition scores, and 53 missing values existed for fluid cognition scores.

UK Biobank: Demographics

We analyzed data from 3,013 participants (1,431 males; 1,582 females) aged 51–83 years (at the time of brain imaging visit) from the UK Biobank dataset. We included participants who had both the required brain imaging data—specifically ASL imaging acquired at time point 0.2, corresponding to the initial imaging session—and peripheral biomarker data. Participants were excluded if they had more than 40 missing values in the brain imaging feature set. Participants with a history of diagnosed mental health conditions were excluded. Excluded mental health conditions included depression, mania, hypomania, bipolar or manic-depression, autism spectrum disorders, panic attacks, obsessive-compulsive disorder (OCD), schizophrenia, personality disorders, and attention deficit disorders (ADD/ADHD). Participants who self-reported neurological or psychiatric illnesses were also excluded. These included Parkinson’s disease, dementia or Alzheimer’s disease, cognitive impairment, multiple sclerosis, other demyelinating diseases, stroke, transient ischemic attack (TIA), ischaemic stroke, epilepsy, brain hemorrhage, subdural or subarachnoid hemorrhage, brain abscess or intracranial abscess, encephalitis, cerebral palsy, cerebral aneurysm, meningitis, meningioma or other benign meningeal tumors, motor neuron disease, nervous system infections, neurological trauma or injury, head injury, acute infective polyneuritis (Guillain-Barré syndrome), spina bifida, and chronic or degenerative neurological problem.

All participants gave written informed consent prior to data collection. All study procedures were conducted in accordance with the principles of the Declaration of Helsinki and were approved by the North-West Multi-Centre Research Ethics Committee (REC references 11/NW/0382, 16/NW/0274, and 21/NW/0157), and these ethical regulations cover the work in this study. The UKBB data was accessed through the approved application number: 45,551. Details on the UK Biobank Ethics and Governance framework are provided at https://www.ukbiobank.ac.uk/media/0xsbmfmw/egf.pdf.

UK Biobank: Brain imaging acquisition

The UK Biobank brain imaging data were acquired using a 3.0 Tesla Siemens Skyra scanner with a standard Siemens 32–channel head coil—across three imaging centers with identical scanners. The imaging acquisition parameters are described in detail at https://biobank.ctsu.ox.ac.uk/crystal/refer.cgi?id=2367 and brain imaging documentation is provided at https://biobank.ctsu.ox.ac.uk/crystal/refer.cgi?id=1977 (also see Miller and colleagues [49]).

T1-weighted structural data were acquired using a 3D MPRAGE sequence with the following parameters: repetition time (TR) =2,000 ms, inversion time (TI) =880 ms, echo times (TE) =2.01 ms, spatial resolution mm3, number of echoes = 4, flip angle , and field of view of mm. T2-weighted fluid-attenuated inversion-recovery (FLAIR) structural data were acquired using a 3D SPACE sequence. Acquisition parameters for the T2-weighted sequence were: TR = 5,000 ms, TE = 395 ms, spatial resolution mm3, turbo factor = 284, and field of view of mm.

Diffusion data were acquired using an EPI sequence with the following parameters: TR = 3,600 ms, flip angle , 50 distinct directions on 2 shells, b = 1,000/2,000 s/mm2, along with 10 b = 0 s/mm2 images, field of view of mm, and imaging matrix of , 72 slices with thickness of 2 mm.

ASL data were acquired using pCASL and a 2D multi-band EPI sequence. Pseudo-continuous ASL data were acquired with labeling duration of 1,800 ms and five post-labeling delays of 400 ms, 800 ms, 1,200 ms, 1,600 ms, and 2,000 ms. One label/control pair per post-labeling delay was acquired. To calibrate perfusion measurements into units of ml/100g/min, one M0 calibration image (effective TR = 5 s) without labeling was also acquired. The spatial resolution for this imaging modality was mm3. Summary measures for blood perfusion and ATT were provided for major brain lobes and subcortical structures. We included 50 ASL-based imaging-derived phenotypes (IDPs) per participant.

UK Biobank: Brain imaging measurements

To relate brain measurements to peripheral biomarkers, we incorporated imaging-derived phenotypes (IDPs) provided by the UK Biobank repository. All IDPs were obtained using the standardized UK Biobank processing pipelines, available at: https://git.fmrib.ox.ac.uk/falmagro/UK_biobank_pipeline_v_1. Specifically, we used diffusion tensor imaging measures (FA, MD), microstructural measures (ISOVF, ICVF), in addition to regional volumes, cortical thickness, cortical surface areas, white matter hyperintensity (WMH), blood perfusion and ATT measures.

Cortical morphometric features—including thickness, surface area, and volume—were extracted using the Desikan–Killiany (DK) atlas (62 parcels). Diffusion-based metrics—including FA, MD, ICVF, and ISOVF—were parcellated using the ICBM-DTI-81 white-matter labels atlas (48 white matter tract labels). We further incorporated 25 regionally defined perfusion- and ATT-related measures. These included values for the right and the left hemispheres’ frontal lobe, occipital lobe, parietal lobe, temporal lobe, cerebellum, caudate, putamen, thalamus, cerebrum white matter and internal carotid artery vascular territory in gray matter. We also used IDPs for mean blood perfusion and ATT in vertebrobasilar arteries vascular territories in gray matter, cerebral white matter with >50% cerebral partial volume, cortical gray matter, and whole-brain gray and white matter.

Subcortical structures were defined using FreeSurfer segmentation (aseg), from which volumetric measures were extracted for the following bilateral regions: accumbens area, thalamus proper, pallidum, putamen, hippocampus, caudate, amygdala, choroid plexus, cerebral white matter, cerebellar white matter, cerebellar cortex, cerebral cortex, and ventral diencephalon. In addition, whole-brain summary measures were included, such as brain stem, BrainSeg, BrainSegNotVent, BrainSegNotVentSurf, total gray matter, and sub-cortical gray matter volumes. We also included subcortical volumes derived from FSL-FIRST for key regions including the accumbens, thalamus, pallidum, putamen, hippocampus, caudate, and amygdala. Regional gray matter volumes were obtained using FSL-FAST for several subcortical areas, including the thalamus, ventral striatum, pallidum, putamen, hippocampus, caudate, and amygdala. Finally, two imaging-derived phenotypes (IDPs) specifically characterizing white matter hyperintensity (WMH) burden were included: total WMH volume estimated from T1- and T2-FLAIR images, and the total volume of white matter hypointensities across the whole brain.

Altogether, the brain feature set included 490 values. We ensured that no subject included in the multi-modal mapping had more than 40 missing values for brain measures; any subject exceeding this threshold was excluded from the analysis.

UK Biobank: Biological samples and vital signs

The UK Biobank dataset included a comprehensive array of participant-specific blood and urine laboratory results in addition to obesity-related measures, blood pressure, and age. The laboratory-based assessments included C-reactive protein, total protein, testosterone, glucose, HbA1c, cholesterol, HDL, LDL, triglycerides, urea, calcium, bilirubin, creatinine, vitamin D, AST, ALT, ALK, sodium urine, potassium urine, and systolic and diastolic blood pressures. Furthermore, participants’ directory included data on biomarkers such as age, BMI, body fat percentage, and waist and hip circumferences. These biomarkers were chosen to mirror those used in the HCP–A dataset, restricted to measures available in the UK Biobank, in order to maximize cross-dataset comparability.

UK Biobank is a longitudinal study; laboratory results were acquired only at the initial assessment visit, while blood pressure and obesity-related measures (e.g., BMI, hip and waist circumferences, and body fat percentage) were acquired at both the initial assessment and the follow-up brain imaging visits. We included age at baseline and age at imaging visit in the original PLS model. In total, 33 biomarkers were included in the analysis for each participant. We also performed an additional PLS analysis in which the effect of age (at imaging visit) was regressed out from all brain imaging and physiological features.

Among the 1,431 male and 1,582 female participants, there were some features with missing values. These were substituted with the median of the sex-specific corresponding columns. For information on number of missing values per biomarker measure see S2 Table.

UK Biobank: Fluid intelligence assessment

All UK Biobank participants completed a fluid intelligence assessment at the time of imaging. The assessment comprised 13 multiple-choice questions administered within a two-minute time frame, and was designed to quantify problem-solving and reasoning abilities in participants. Questions were presented individually on screen with 3–5 response options. For each question, participants could select their chosen answer, or “Do not know”, and “Prefer not to answer” alternatives. The assessment evaluated verbal reasoning (e.g., analogical relationships: “Bud is to flower as child is to...?” with options including Grow, Develop, Improve, Adult, Old) and numerical reasoning (e.g., sequence completion: “150...137...125...114...104... What comes next?” with options 96, 95, 94, 93, 92). The fluid intelligence score was calculated as the total number of correct responses within the two-minute limit [231].

When calculating correlations between PLS scores and fluid intelligence scores, data from individuals with missing fluid intelligence scores were excluded. Missing scores totaled 121 among males and 159 among females.

Atlases

Cortical features in the HCP–Aging dataset were extracted using the Schaefer-400 functional atlas [65]. White matter features were extracted using the Johns Hopkins University (JHU) white-matter tractography atlas (threshold 25%) [66,67]. WMH values were obtained using the Hammer atlas available at https://zenodo.org/records/7930159.

In the UK Biobank dataset, cortical thickness and surface area were provided for each parcel of the Desikan-Killiany-Tourville (DKT) atlas. This information was derived using the FreeSurfer v6.0.0. For cortical blood perfusion and arterial transit time, broader anatomical labels (frontal lobe, insula, occipital cortex, parietal lobe, and temporal lobe) were used due to the low spatial resolution of the ASL imaging.

Regional subcortical volumes in the UK Biobank were obtained with the Functional Magnetic Resonance Imaging of the Brain (FMRIB)’s Integrated Registration and Segmentation Tool (FIRST). For subcortical cerebral blood perfusion and arterial transit time, only major structures such as caudate, cerebellum, and thalamus were included.

In UK Biobank data, FA, MD, ICVF, and ISOVF measures were summarized across 48 standard parcels of the JHU atlas.

Cortical thickness

Cortical thickness quantifies the width of cortical gray matter. The individual-level cortical thickness maps in HCP–A dataset were derived through the HCP Minimal Preprocessing Pipeline [227]. In short, this pipeline used both participant-specific bias-corrected T1- and T2-weighted structural data to segment the cortical gray and white matter and performed a surface reconstruction using FreeSurfer. Next, cortical thickness was estimated as the geometric distance between the white and pial surfaces. The individual-level cortical thickness maps in UK Biobank were also constructed by incorporating both T1- and T2-weighted structural data using the FreeSurfer pipeline.

Cortical myelin

T1/T2 ratio quantifies the cortical myelin profile. T1/T2 ratio is affected by the microstructural characteristics of cortical gray matter. Division the T1-weighted image by the T2-weighted image enhances myelin contrast to noise ratio [232,233]. Specifically, we used the RF transmit (B1+) field corrected myelin maps following recommendations from Glasser and colleagues [234]. Myelin was only assessed in HCP–A dataset.

Fractional anisotropy and mean diffusivity

Fractional anisotropy (FA) quantifies the anisotropy of water diffusion, and ranges from 0 to 1. FA = 1 indicates that within the region of interest, all water movements occur in the same direction, while FA = 0 indicates that there is no dominant directionality in the movements of water molecules. In other words, FA is a measure that examines the “relative” directional water diffusion along the principal axis of diffusion versus diffusion in other directions. Higher FA may indicate greater fiber density, lower membrane permeability, or greater myelin. Higher FA can also be a result of disproportionate decrease in one or more of the non-dominant fiber bundles. Notably, constant FA of a region is not indicative of unchanged underlying tissue; in a case where bundles within a region are all damaged in the same way, FA—which is a relative measure of water diffusivity—stays constant [235].

Mean diffusivity (MD) quantifies the overall diffusivity of water within a region of interest (mean of diffusion along the three tensor dimensions). MD quantification is more robust and interpretable (than FA) in the presence of crossing fibers, and can assess how the tissue is constraining the water diffusion in a region of interest [235].

Both FA and MD measures were derived from diffusion tensor imaging. Cortical FA and MD were only assessed in HCP–A dataset, while white matter FA and MD were assessed in both datasets.

Functional connectivity strength

Functional connectivity (FC) quantifies the synchronization of fluctuation in BOLD signals across brain regions. Functional MRI data were preprocessed using the HCP Minimal Preprocessing Pipeline. For detailed preprocessing steps, refer to the cited reference [227]. The vertex-wise functional MRI time-series were initially demeaned and subsequently parcellated using the Schaefer-400 functional atlas [65]. The parcellated time-series were then z-scored and concatenated across participant runs. Each participant’s unified time-series was used to derive a functional connectivity matrix. The functional connectome was computed by calculating the Pearson correlation coefficient between pairs of regional time-series. To construct the functional connectivity strength map, we computed the absolute value of all functional connectivity edges and summed the edges connected to each region for each participant (an array of size 400 per participant). FC strength was only assessed in HCP–A dataset.

Structural connectivity strength

Structural connectivity (SC) quantifies the density of white matter tracts across brain regions. Diffusion MRI data were preprocessed using the HCP Minimal Preprocessing Pipeline. We next used probtrackx to build the participant-specific connectomes using the Schaefer-400 cortical parcellation. We used the default settings when running probtrackx. To construct the structural connectivity strength map, we computed the absolute value of all structural connectivity edges and summed the edges connected to each region for each participant (an array of size 400 per participant). SC strength was only assessed in HCP–A dataset.

White matter hyperintensity

White matter hyperintensities (WMHs) are regions detectable on structural brain MRI, appearing hyperintense on T2-weighted and fluid-attenuated inversion-recovery (FLAIR) images, and hypointense on T1-weighted images. They are associated with microangiopathy and chronic ischemia. Histopathological studies indicate that WMHs reflect tissue damage ranging from slight disentanglement of the matrix to varying degrees of myelin and axonal loss [236].

In HCP–A dataset, BISON (Brain tISsue segmentatiON) automatic segmentation tool was used to segment WMHs [237]. BISON combined a random forest classifier with a collection of location and intensity features obtained from a library of manually segmented scans to detect WMHs. T2-weighted and T1-weighted images were utilized for WMH segmentation in HCP–A. The WMH segmentations were visually quality controlled by an experienced rater (R.M.). The number of voxels designated as WMH (measured in mm3 in the standard space; i.e., adjusted for intracranial volume) in each brain lobe and hemisphere (based on Hammer’s lobar atlas) as well as across the entire brain were used to define regional and global WMH volumes, respectively. WMH volumes were log-transformed to obtain a normal distribution.

In UK Biobank, we used two IDPs to quantify ischemia-related structural changes: total volume of white matter hyperintensities from T2 FLAIR and T1 images [238], and volume of white matter hypointensities in the whole brain, generated based on T1 images.

Intracellular volume fraction and isotropic volume fraction

Intracellular volume fraction (ICVF) quantifies the density of neurites (axons and dendrites). Isotropic volume fraction (ISOVF) quantifies the proportion of free water (extracellular water diffusion). Higher ICVF and lower ISOVF indicate better tissue microstructural organization. These measures were calculated by feeding the diffusion MRI data in the Neurite Orientation Dispersion and Density Imaging (NODDI) modeling using the Accelerated Microstructure Imaging via Convex Optimization (AMICO) tool [239,240]. ICVF and ISOVF were only assessed in the UK Biobank dataset.

Partial least squares

Partial least squares (PLS) analysis was performed using the pyls toolbox (https://github.com/netneurolab/pypyls). PLS analysis is a technique used to capture the multivariate relationship between two data matrices (not necessarily the causal effect between the datasets) [4345]. In this report, the investigated data matrices were “brain imaging feature maps” () and peripheral biomarkers (). Each column in each data matrix was first z-scored; next, the covariance (correlation) between normalized brain imaging features (X) and biomarkers (Y) was computed. The covariance matrix was decomposed () using the singular value decomposition (SVD):

(1)

here U and V were orthonormal matrices of left and right singular vectors and S was a diagonal matrix of singular values. Each triplet of a left singular vector, a right singular vector, and a singular value constituted a latent variable. Singular vectors weighted the contribution of original features (regional brain imaging features and biomarkers) to the overall multivariate pattern. To quantify the extent to which individual participants expressed the multivariate pattern captured by a latent variable, participant-specific brain imaging and biomarker scores were calculated. Scores were computed by projecting the original data onto the respective singular vector weights, such that each individual was assigned a brain imaging score and a biomarker score:

(2)(3)

Next, PLS loadings for a latent variable were computed by calculating the Pearson’s correlation between participant-specific biomarker measures (or brain imaging measures) and the respective score pattern. The proportion of covariance explained by each latent variable was quantified as the ratio of the squared singular value to the sum of all squared singular values. The statistical significance of each latent variable was determined by permutation test. The testing process involved randomly permuting the order of observations (i.e., rows) of data matrix X for a total of 1,000 repetitions, followed by constructing a set of “null” brain–biomarker correlation matrices. These “null” correlation matrices were then subjected to SVD, to generate a distribution of singular values under the null hypothesis that there was no association between brain imaging features’ pattern and participants’ biomarkers. A non-parametric p-value could be estimated for each given latent variable as the probability that a permuted singular value exceeds the original, non-permuted singular value.

The reliability of individual biomarker contribution to the latent variable was evaluated using bootstrap resampling. Participants (rows of data matrices X and Y) were randomly sampled with replacement across 1,000 repetitions, resulting in a new set of correlation matrices that were subsequently subjected to SVD. This procedure generated a sampling distribution for each individual weight in the singular vectors. For each biomarker, a bootstrap ratio was computed as the ratio of its singular vector weight to its bootstrap-estimated standard error. High bootstrap ratios indicated biomarkers that significantly contribute to the latent variable and are stable across participants.

Finally, we used cross-validation to assess the generalizability of PLS results [241,242]. We assessed the out-of-sample correlation between brain imaging features and biomarker scores. We used 100 randomized train-test splits of the dataset; in each random split, we used 80% of the data for training and 20% of the data for testing. In each iteration, PLS was applied to the training data (Xtrain and Ytrain) to estimate singular vector weights (Utrain and Vtrain); test data were then projected onto these derived weights to compute participant-specific scores ( and ). The correlation between brain and biomarker scores was evaluated for the test sample. This procedure led to 100 correlation values and established a distribution of out-of-sample correlation values. To assess the statistical significance of these out-of-sample correlation values, we conducted permutation tests (100 repetitions). During each permutation, we shuffled the matrix rows and repeated the analysis to create a null distribution of correlation coefficients between brain imaging and physiological scores in the test sample. This null distribution was then used to estimate a non-parametric p-value, by calculating the proportion of null correlation coefficients that were greater than or equal to the mean original out-of-sample correlation coefficient.

Generalized additive model for location, scale, and shape

Generalized additive model for location, scale, and shape (GAMLSS) was implemented using the gamlss R package available at https://github.com/gamlss-dev [90]. We used a sex-stratified GAMLSS modeling approach to regress out the non-linear effect of age from features including brain measurements, peripheral biomarkers and cognitive scores. In this framework, each feature of interest is assumed to be a random variable (Y) following the normal distribution ():

(4)

here, the distribution parameters of —mean (), standard deviation ()—are modeled as the fractional polynomial functions of the explanatory variable (age; x). We used the fp() function to determine the best-fitting two-term fractional polynomials from the predefined set of power values: . The optimal set of powers is chosen automatically through iterative model fitting to best capture non-linear relationships between age and distribution parameters.

For the UK Biobank dataset, we regressed out the effects of both age and imaging center by using non-linear models that included center ID as a fixed covariate. This ensured that remaining variation in the features reflected neither age nor center-related biases.

Statistics and null models

To assess the effect of spatial autocorrelation on spatial associations between two cortical brain maps, we used two null models, the so-called spatial autocorrelation preserving permutation tests, commonly referred to as “spin tests” [243] and variogram-estimating null models, referred to as the BrainSMASH method. To implement spin tests, brain phenotypes were projected onto the spherical projection of the fsaverage surface. This involved selecting the coordinates of the vertex closest to the center of mass for each parcel. These parcel coordinates were then randomly rotated, and original parcels were reassigned to the value of the closest rotated parcel (N repetitions; throughout the manuscript N = 1,000). For parcels for which the medial wall was closest, we assigned the value of the next closest parcel instead. Following these steps, we obtained a series of randomized brain maps that have the same values and spatial autocorrelation as the original map but where the relationship between values and their spatial location had been permuted. These maps were then used to generate null distributions of desired statistics. To implement variogram-estimating null models, first the values in a given brain map were randomly permuted, then the permuted values were smoothed and rescaled to reintroduce spatial autocorrelation characteristic of the original, non-permuted map (throughout the manuscript N = 1,000) [244]. Reintroduction of spatial autocorrelation onto the permuted data is achieved via the following transformation , where is the permuted data, is Gaussian noise, and and are estimated via a least-squares optimization to match the variogram of the original data and the permuted data. The resulting maps were then used to generate null distributions of desired statistics. Both spin tests and BrainSMASH were implemented using the neuromaps toolbox (available at https://github.com/netneurolab/neuromaps) [245].

Throughout the manuscript, spatial correspondence between cortical brain maps (in HCP–A dataset) was assessed after parcellation using the Schaefer-400 cortical atlas [65]. Notably, this parcellation was chosen because it divides the cortex into relatively homogeneous parcel sizes, and its number of parcels was comparable to the estimated number of distinct human neocortical areas [246,247].

To assess the statistical significance of the association between cognitive scores and PLS brain scores, we performed permutation testing. We first calculated Spearman’s rank correlation between the observed cognitive scores and PLS brain scores. Next, we permuted the cognitive scores 1,000 times and recalculated the correlation for each permutation to generate a null distribution. Two-sided, non-parametric p-values were then derived by comparing the observed correlation against this null distribution.

Furthermore, significance of PLS latent variables was assessed by permutation tests. The generalization of PLS results was assessed using cross-validation approach; see Methods: Partial least squares for more details. Note that throughout the manuscript, statistical significance was assumed at p-value less than 0.05.

Datasets and code

The code to obtain the results within this manuscript relies on open-source Python packages including NumPy (version 1.21.6) [248,249], SciPy (version 1.7.3) [250], pandas (version 1.3.5) [251], seaborn (version 0.12.2) [252], Matplotlib (version 3.5.3) [253], statsmodels (version 0.13.5) [254], bctpy (version 0.6.1) [255], Nilearn (version 0.10.1, see [256]), NiBabel (version 4.0.2) [257], netneurotools (version 0.2.3) [258], neuromaps (version 0.0.4) [245], and rpy2 (version 3.5.17) [259].

Parcellation atlases, including the Schaefer-400 functional atlas [65], and Johns Hopkins University (JHU) white matter tractography atlas [66,67], can be obtained from https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations, and https://web.mit.edu/fsl_v5.0.10/fsl/doc/wiki/Atlases.html, respectively. The GAMLSS models are implemented using GAMLSS R package (version ) available at https://github.com/gamlss-dev [90]. The PLS analysis is performed using the pyls toolbox (version 0.0.1) available at https://github.com/netneurolab/pypyls. All brain plots in the manuscript are visualized using Connectome Workbench (version 1.5.0), available at https://www.humanconnectome.org/software/get-connectome-workbench [260].

Supporting information

S2 Fig. UK Biobank biomarkers versus age.

Relationship between participants’ age at the time of brain imaging (x-axis) and raw biomarker values (y-axis) (blue: male, red: female). For biomarkers measured at both initial assessment and follow-up imaging visits, values corresponding to the imaging visit are denoted with the subscript “2”.

https://doi.org/10.1371/journal.pbio.3003856.s002

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S5 Fig. Statistical comparison of absolute brain loading values for the first latent variable.

Horizontal lines indicate statistical significance (p < 0.05, FDR-corrected). Black dots represent mean absolute loading values. Also see Fig 1B.

https://doi.org/10.1371/journal.pbio.3003856.s005

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S8 Fig. Similarity of first latent variable brain loadings between males and females.

(a) Cortical brain loadings comparison. In the scatter plots, each dot represents a cortical brain region defined by the Schaefer-400 parcellation; the dots are color-coded based on the Yeo-7 functional resting-state networks. The x-axis shows male brain loadings and the y-axis shows female brain loadings. Green asterisks indicate significant associations where the significance of empirical correlation is assessed using spin tests (pspin<0.05) and orange asterisks indicate significant associations where the significance of empirical correlation is assessed using variogram-estimating null models (pSMASH<0.05). (b) White matter tract loadings comparison. The scatter plots show the similarity of brain loadings between males (x-axis) and females (y-axis) for white matter tract measures, including blood perfusion, arterial transit time (ATT), fractional anisotropy (FA), and mean diffusivity (MD). (c) White matter hyperintensity loadings comparison. The scatter plot shows the similarity of brain loadings between males (x-axis) and females (y-axis) for the white matter hyperintensity measure.

https://doi.org/10.1371/journal.pbio.3003856.s008

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S9 Fig. Statistical comparison of absolute brain loading values for the second latent variable.

Blood perfusion loadings have the greatest absolute values among all brain measures examined. Horizontal lines indicate statistical significance (p < 0.05, FDR-corrected). Black dots represent mean absolute loading values. Also see Fig 3B.

https://doi.org/10.1371/journal.pbio.3003856.s009

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S11 Fig. Similarity of second latent variable brain loadings between males and females.

(a) Cortical brain loadings comparison. In the scatter plots, each dot represents a cortical brain region defined by the Schaefer-400 parcellation; the dots are color-coded based on the Yeo-7 functional resting-state networks. The x-axis shows male brain loadings and the y-axis shows female brain loadings. Green asterisks indicate significant associations where the significance of empirical correlation is assessed using spin tests (pspin<0.05) and orange asterisks indicate significant associations where the significance of empirical correlation is assessed using variogram-estimating null models (pSMASH<0.05). (b) White matter tract loadings comparison. The scatter plots show the similarity of brain loadings between males (x-axis) and females (y-axis) for white matter tract measures, including blood perfusion, arterial transit time (ATT), fractional anisotropy (FA), and mean diffusivity (MD). (c) White matter hyperintensity loadings comparison. The scatter plot shows the similarity of brain loadings between males (x-axis) and females (y-axis) for white matter hyperintensity measure.

https://doi.org/10.1371/journal.pbio.3003856.s011

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S12 Fig. LV–I brain loadings - no age effect.

(a) Brain loadings for each included brain feature. This indicates that participants who more strongly express the biomarker pattern illustrated in Fig 5A (e.g., those with greater BMI) have lower blood perfusion. Brain maps are shown on the fsLR inflated cortical surfaces. (b) Similarity of brain loadings across included brain features. Associations that remain significant after controlling for spatial autocorrelation and false discovery rate (FDR) correction are marked with their corresponding correlation values. Green asterisks indicate significant associations where the significance of empirical correlation is assessed using spin tests (pspin<0.05) and orange asterisks indicate significant associations where the significance of empirical correlation is assessed using variogram-estimating null models (pSMASH<0.05) (FC and blood perfusion: pspin = 0.042, pSMASH>0.05 (males), , pSMASH>0.05 (females); FA and MD: , (males), pspin = 0.014, pSMASH = 0.014 (females); FA and SC: , (males), pspin = 0.014, pSMASH = 0.014 (females); myelin and SC: , (males); ATT and FC: , pSMASH>0.05 (males); thickness and myelin: pspin = 0.042, pSMASH>0.05 (males); thickness and FA: pspin = 0.042, pSMASH>0.05 (females); ATT and thickness: pspin>0.05, pSMASH = 0.021 (males)).

https://doi.org/10.1371/journal.pbio.3003856.s012

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S13 Fig. Similarity of first latent variable brain loadings between males and females - no age effect.

(a) Cortical brain loadings comparison. In the scatter plots, each dot represents a cortical brain region defined by the Schaefer-400 parcellation; the dots are color-coded based on the Yeo-7 functional resting-state networks. The x-axis shows male brain loadings and the y-axis shows female brain loadings. Green asterisks indicate significant associations where the significance of empirical correlation is assessed using spin tests (pspin<0.05) and orange asterisks indicate significant associations where the significance of empirical correlation is assessed using variogram-estimating null models (pSMASH<0.05). (b) White matter tract loadings comparison. The scatter plots show the similarity of brain loadings between males (x-axis) and females (y-axis) for white matter tract measures, including blood perfusion, arterial transit time (ATT), fractional anisotropy (FA), and mean diffusivity (MD). (c) White matter hyperintensity loadings comparison. The scatter plot shows the similarity of brain loadings between males (x-axis) and females (y-axis) for the white matter hyperintensity measure.

https://doi.org/10.1371/journal.pbio.3003856.s013

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S14 Fig. Statistical comparison of absolute brain loading values for the first latent variable - no age effect.

Blood perfusion loadings have the greatest absolute values among all brain measures examined. Horizontal lines indicate statistical significance (p < 0.05, FDR-corrected). Black dots represent mean absolute loading values. Also see Fig 5B.

https://doi.org/10.1371/journal.pbio.3003856.s014

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S15 Fig. Mapping biomarkers to brain features in the UK Biobank dataset: first latent variable (LV–I) captures the aging axis.

Using PLS analysis, we identify a significant latent variable that accounts for 75.71% (males) and 78.11% (females) of the covariance in the data. The PLS model includes 33 features on the biomarker side and 490 features on the brain side. (a) Biomarker loadings. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Each biomarker loading is divided by its bootstrap-estimated standard error, yielding a measure called “bootstrap ratio”. Bootstrap ratio is high for biomarkers with large weights and small standard errors. Stable biomarkers for which the estimated 95% confidence intervals do not cross zero, are shown in red. BMI, body fat percentage, age, hip and waist circumference were collected at both initial assessment and imaging visits. Variables measured in the imaging visit are denoted with a subscript 2 (e.g., BMI2), while baseline values are written without subscripts. Subscript 1 is used to indicate repeated measurements (e.g., systolic blood pressure1). (b) Brain loadings. Each dot represents a brain region (cortical, subcortical, or a white matter tract). (c) Correlation between brain (x-axis) and biomarker scores (y-axis) for males (top; r = 0.63) and females (bottom; r = 0.59). The score per participant shows the extent to which the participant expresses the brain–biomarker association captured by LV–I. Each dot represents an individual participant, colored by their age at imaging time point. Score correlation values passed cross-validation in both sex groups.

https://doi.org/10.1371/journal.pbio.3003856.s015

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S17 Fig. Mapping biomarkers to brain features in the UK Biobank dataset: second latent variable (LV–II) captures the metabolic axis.

Using PLS analysis, we identify a significant latent variable that accounts for 15.33% (males) and 14.93% (females) of the covariance in the data. The PLS model includes 33 features on the biomarker side and 490 features on the brain side. (a) Biomarker loadings. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Each biomarker loading is divided by its bootstrap-estimated standard error, yielding a measure called “bootstrap ratio”. Bootstrap ratio is high for biomarkers with large weights and small standard errors. Stable biomarkers for which the estimated 95% confidence intervals do not cross zero, are shown in red. BMI, body fat percentage, age, hip and waist circumference were collected at both initial assessment and imaging visits. Variables measured in the imaging visit are denoted with a subscript 2 (e.g., BMI2), while baseline values are written without subscripts. Subscript 1 is used to indicate repeated measurements (e.g., systolic blood pressure1). (b) Brain loadings. Each dot represents a brain region (cortical, subcortical, or a white matter tract). (c) Correlation between brain (x-axis) and biomarker scores (y-axis) for males (top; r = 0.35) and females (bottom; r = 0.36). Each dot represents an individual participant, colored by their BMI at imaging time point. The scores per participant show the extent to which the participant expresses the brain–biomarker association captured by LV–II. Score correlation values passed cross-validation in both sex groups.

https://doi.org/10.1371/journal.pbio.3003856.s017

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S18 Fig. Statistical comparison of absolute brain loading values for the second latent variable in UK Biobank.

Blood perfusion loadings have the greatest absolute values among all brain measures examined. Horizontal lines indicate statistical significance (p < 0.05, FDR-corrected). Black dots represent mean absolute loading values. Also see S17B Fig.

https://doi.org/10.1371/journal.pbio.3003856.s018

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S19 Fig. Mapping biomarkers to brain features after regressing out the age effect in the UK Biobank dataset: first latent variable (LV–I) captures the metabolic axis.

Using PLS analysis, we identify a significant latent variable that accounts for 65.31% (males) and 60.37% (females) of the covariance in the data. The PLS model includes 33 features on the biomarker side and 490 features on the brain side. (a) Biomarker loadings. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Each biomarker loading is divided by its bootstrap-estimated standard error, yielding a measure called “bootstrap ratio”. Bootstrap ratio is high for biomarkers with large weights and small standard errors. Stable biomarkers for which the estimated 95% confidence intervals do not cross zero, are shown in red. BMI, body fat percentage, age, hip and waist circumference were collected at both initial assessment and imaging visits. Variables measured in the imaging visit are denoted with a subscript 2 (e.g., BMI2), while baseline values are written without subscripts. Subscript 1 is used to indicate repeated measurements (e.g., systolic blood pressure1). (b) Brain loadings. Each dot represents a brain region (cortical, subcortical, or a white matter tract). (c) Correlation between brain (x-axis) and biomarker scores (y-axis) for males (top; r = 0.40) and females (bottom; r = 0.38). Each dot represents an individual participant, colored by their BMI at imaging visit. The score per participant shows the extent to which the participant expresses the brain–biomarker association captured by LV–I. Score correlation values passed cross-validation in both sex groups.

https://doi.org/10.1371/journal.pbio.3003856.s019

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S20 Fig. Statistical comparison of absolute brain loading values for the first latent variable in UK Biobank - no age effect.

Blood perfusion loadings have the greatest absolute values among all brain measures examined. Horizontal lines indicate statistical significance (p < 0.05, FDR-corrected). Black dots represent mean absolute loading values. Also see S19B Fig.

https://doi.org/10.1371/journal.pbio.3003856.s020

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S21 Fig. Cognitive relevance of metabolic axis in UK Biobank.

The left scatter plot shows data for males () and the right scatter plot shows data for females () (Nperm = 1,000). Brain scores are derived from the analysis presented in S19 Fig. Fitted regression lines are shown in blue for males and in red for females.

https://doi.org/10.1371/journal.pbio.3003856.s021

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S22 Fig. Generalization of HCP–A-derived PLS latent variables to the UK Biobank cohort.

We identify brain features and biomarkers shared across the HCP–A and UK Biobank datasets. We use these features to construct sex-stratified PLS models based on the HCP–A data. (a) Biomarker loadings of the first latent variable. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Stable biomarkers are shown in red. (b) Brain loadings of the first latent variable. Each bar represents a global brain feature. (c) Using the weights of the PLS models, we mapped the UK Biobank data into the HCP–A-derived latent space. For the first latent variable, significant correlations between projected brain and biomarker scores are observed for males (top; r = 0.41, ) and females (bottom; r = 0.46, ). (d) Biomarker loadings of the second latent variable. (e) Brain loadings of the second latent variable. (f) Using the weights of the PLS models, we mapped the UK Biobank data into the HCP–A-derived latent space. For the second latent variable, significant correlations between projected brain and biomarker scores are observed for males (top; r = 0.12, ) and females (bottom; r = 0.13, ).

https://doi.org/10.1371/journal.pbio.3003856.s022

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S23 Fig. Mapping biomarkers to reduced brain features in the HCP–A dataset: first latent variable (LV–I) captures the aging axis.

Using PLS analysis, we identify a significant latent variable that accounts for 82.87% (males) and 83.89% (females) of the covariance between brain measurements and biomarkers. The PLS model includes 28 features on the biomarker side and 13 features on the brain side. (a) Biomarker loadings. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Stable biomarkers for which the estimated 95% confidence intervals do not cross zero, are shown in red. (b) Brain loadings. Each bar represents a global brain measure. (c) Correlation between brain (x-axis) and biomarker scores (y-axis) for males (top; r = 0.72) and females (bottom; r = 0.68). Each dot represents an individual participant, colored by their age. Score correlation values passed cross-validation in both sex groups (for both: ).

https://doi.org/10.1371/journal.pbio.3003856.s023

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S24 Fig. Mapping biomarkers to reduced brain features in the HCP–A dataset: second latent variable (LV–II) captures the metabolic axis.

Using PLS analysis, we identify a significant latent variable that accounts for 10.29% (males) and 10.79% (females) of the covariance between brain measurements and biomarkers. The PLS model includes 28 features on the biomarker side and 13 features on the brain side. (a) Biomarker loadings. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Stable biomarkers for which the estimated 95% confidence intervals do not cross zero, are shown in red. (b) Brain loadings. Each bar represents a global brain measure. (c) Correlation between brain (x-axis) and biomarker scores (y-axis) for males (top; r = 0.48) and females (bottom; r = 0.50). Each dot represents an individual participant, colored by their BMI. Score correlation values passed cross-validation in both sex groups (for both: ).

https://doi.org/10.1371/journal.pbio.3003856.s024

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S25 Fig. Mapping biomarkers to reduced brain features in the UK Biobank dataset: first latent variable (LV–I) captures the aging axis.

Using PLS analysis, we identify a significant latent variable that accounts for 84.16% (males) and 87.21% (females) of the covariance between brain measurements and biomarkers. The PLS model includes 33 features on the biomarker side and 11 features on the brain side. (a) Biomarker loadings. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Stable biomarkers for which the estimated 95% confidence intervals do not cross zero, are shown in red. (b) Brain loadings. Each bar represents a global brain measure. (c) Correlation between brain (x-axis) and biomarker scores (y-axis) for males (top; r = 0.60) and females (bottom; r = 0.57). Each dot represents an individual participant, colored by their age. Score correlation values passed cross-validation in both sex groups (for both: ).

https://doi.org/10.1371/journal.pbio.3003856.s025

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S26 Fig. Mapping biomarkers to reduced brain features in the UK Biobank dataset: second latent variable (LV–II) captures the metabolic axis.

Using PLS analysis, we identify a significant latent variable that accounts for 11.12% (males) and 9.10% (females) of the covariance between brain measurements and biomarkers. The PLS model includes 33 features on the biomarker side and 11 features on the brain side. (a) Biomarker loadings. Bootstrap resampling is used to estimate the stability of each individual biomarker’s contribution to the overall multivariate pattern. Stable biomarkers for which the estimated 95% confidence intervals do not cross zero, are shown in red. (b) Brain loadings. Each bar represents a global brain measure. (c) Correlation between brain (x-axis) and biomarker scores (y-axis) for males (top; r = 0.27) and females (bottom; r = 0.24). Each dot represents an individual participant, colored by their BMI. Score correlation values passed cross-validation in both sex groups (for both: ).

https://doi.org/10.1371/journal.pbio.3003856.s026

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S27 Fig. Individual variability in brain outcomes in metabolic syndrome.

Not all individuals exposed to metabolic dysfunction experience equivalent brain outcomes. (a) Brain and biomarker scores for LV–II in HCP–A, (b) and in UK Biobank. Some individuals show elevated metabolic dysfunction on the biomarker side but relatively preserved or less affected brain signatures. These individuals fall below the main brain–biomarker regression line (pink dots), and represent a resilient phenotype, in which the brain appears comparatively protected relative to metabolic risk. Conversely, some individuals show adverse brain metabolic signatures despite only moderate peripheral risk (gray dots). These cases reflect a vulnerable phenotype, in which the brain is particularly sensitive to metabolic perturbations. On the leftmost panel, we highlight two male participants from the HCP–A cohort with comparable biomarker scores but divergent brain scores. The participant shown in blue has a smaller brain score and the one in red has a higher brain score, meaning that despite similar peripheral metabolic profiles, the participant shown in red has greater brain vulnerability.

https://doi.org/10.1371/journal.pbio.3003856.s027

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S2 Table. Biomarkers in UK Biobank.

For each biomarker, the table reports the acquisition session and the number of participants with missing values (not-a-number). Body mass index, body fat percentage, age, hip and waist circumference were measured at both the initial assessment and the imaging visits. Variables acquired during the imaging visit are denoted as 2.0 in the “Time point” column, while values acquired during the initial assessment are denoted as 0.0. A value of 0.1 indicates values acquired during the repeated assessment visit.

https://doi.org/10.1371/journal.pbio.3003856.s029

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Acknowledgments

We thank all participants and staff of the HCP–A and UK Biobank datasets. We thank Justine Hansen, Vincent Bazinet, Filip Milisav, Yigu Zhou, Tahmineh Taheri, and Moohebat Pourmajidian for their comments and suggestions on the manuscript.

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