Multivariate Analysis and Modelling of multiple Brain endOphenotypes: Let's MAMBO!

Compositional brain scores capture Alzheimer's disease-specific structural brain patterns along the disease continuum

INTRODUCTION

Traditional multivariate methods for neuroimaging studies overlook the interdependent relationship between brain features. This study addresses this gap by analyzing relative brain volumetric patterns to capture how Alzheimer's disease (AD) and genetics influence brain structure along the disease continuum.

METHODS

This study analyzed data from participants across the AD continuum from the Alzheimer's and Families (ALFA) and Alzheimer's Disease Neuroimaging Initiative (ADNI) studies. Compositional data analysis (CoDA) was exploited to examine relative brain volumetric variations that (1) were linked to different AD stages compared to cognitively unimpaired amyloid-β-negative (CU A-) individuals and (2) varied by AD genetic risk.

RESULTS

Disease stage-specific compositional brain scores were identified, differentiating CU A- individuals from those in more advanced stages. Genetic risk-stratified models revealed a broader genetic landscape affecting brain morphology in AD, beyond the well-known apolipoprotein E ε4 allele.

DISCUSSION

CoDA emerges as an alternative multivariate framework to deepen understanding of AD-related structural changes and support targeted interventions for those at higher genetic risk.

HIGHLIGHTS

Compositional data analysis (CoDA) revealed the relative variation of brain region volumes, captured in compositional brain scores, capable of discerning between cognitively unimpaired amyloid-β-negative individuals and subjects within other disease-stage groups along the Alzheimer's disease (AD) continuum. CoDA also uncovered the genetic vulnerability of specific brain regions at each stage of the disease along the continuum. CoDA is capable of integrating magnetic resonance imaging data from two different cohorts without stringent requirements for harmonization. This translates as an advantage, compared to traditional methods, and strengthens the reliability of cross-study comparisons by standardizing the data despite different labeling agreements, facilitating collaborative and large-scale research. The algorithm is sensitive to AD-specific effects, as the main compositional brain scores display little overlap with the age-specific compositional brain score. CoDA provides a more accurate analysis of brain imaging data addressing its compositional nature, which can influence the development of targeted approaches, opening new avenues for enhancing brain health.

Compositional structural brain signatures capture Alzheimer's genetic risk on brain structure along the disease continuum

INTRODUCTION

Traditional brain imaging genetics studies have primarily focused on how genetic factors influence the volume of specific brain regions, often neglecting the overall complexity of brain architecture and its genetic underpinnings.

METHODS

This study analyzed data from participants across the Alzheimer's disease (AD) continuum from the ALFA and ADNI studies. We exploited compositional data analysis to examine relative brain volumetric variations that (i) differentiate cognitively unimpaired (CU) individuals, defined as amyloid-negative (A-) based on CSF profiling, from those at different AD stages, and (ii) associated with increased genetic susceptibility to AD, assessed using polygenic risk scores.

RESULTS

Distinct brain signatures differentiated CU A-individuals from amyloid-positive MCI and AD. Moreover, disease stage-specific signatures were associated with higher genetic risk of AD.

DISCUSSION

The findings underscore the complex interplay between genetics and disease stages in shaping brain structure, which could inform targeted preventive strategies and interventions in preclinical AD.

Identifying the joint signature of brain atrophy and gene variant scores in Alzheimer's Disease

The joint modeling of genetic data and brain imaging information allows for determining the pathophysiological pathways of neurodegenerative diseases such as Alzheimer's disease (AD). This task has typically been approached using mass-univariate methods that rely on a complete set of Single Nucleotide Polymorphisms (SNPs) to assess their association with selected image-derived phenotypes (IDPs). However, such methods are prone to multiple comparisons bias and, most importantly, fail to account for potential cross-feature interactions, resulting in insufficient detection of significant associations. Ways to overcome these limitations while reducing the number of traits aim at conveying genetic information at the gene level and capturing the integrated genetic effects of a set of genetic variants, rather than looking at each SNP individually. Their associations with brain IDPs are still largely unexplored in the current literature, though they can uncover new potential genetic determinants for brain modulations in the AD continuum. In this work, we explored an explainable multivariate model to analyze the genetic basis of the grey matter modulations, relying on the AD Neuroimaging Initiative (ADNI) phase 3 dataset. Cortical thicknesses and subcortical volumes derived from T1-weighted Magnetic Resonance were considered to describe the imaging phenotypes. At the same time the genetic counterpart was represented by gene variant scores extracted by the Sequence Kernel Association Test (SKAT) filtering model. Moreover, transcriptomic analysis was carried on to assess the expression of the resulting genes in the main brain structures as a form of validation. Results highlighted meaningful genotype-phenotype interactionsas defined by three latent components showing a significant difference in the projection scores between patients and controls. Among the significant associations, the model highlighted EPHX1 and BCAS1 gene variant scores involved in neurodegenerative and myelination processes, hence relevant for AD. In particular, the first was associated with decreased subcortical volumes and the second with decreasedtemporal lobe thickness. Noteworthy, BCAS1 is particularly expressed in the dentate gyrus. Overall, the proposed approach allowed capturing genotype-phenotype interactions in a restricted study cohort that was confirmed by transcriptomic analysis, offering insights into the underlying mechanisms of neurodegeneration in AD in line with previous findings and suggesting new potential disease biomarkers.

A fast non-parametric test of association for multiple traits

The increasing availability of multidimensional phenotypic data in large cohorts of genotyped individuals requires efficient methods to identify genetic effects on multiple traits. Permutational multivariate analysis of variance (PERMANOVA) offers a powerful non-parametric approach. However, it relies on permutations to assess significance, which hinders the analysis of large datasets. Here, we derive the limiting null distribution of the PERMANOVA test statistic, providing a framework for the fast computation of asymptotic p values. Our asymptotic test presents controlled type I error and high power, often outperforming parametric approaches. We illustrate its applicability in the context of QTL mapping and GWAS.

Inferring the Genetic Influences on Psychological Traits Using MRI Connectivity Predictive Models: Demonstration with Cognition

Introduction

Genetic correlations between brain and behavioral phenotypes in analyses from major genetic consortia have been weak and mostly nonsignificant. fMRI models of systems-level brain patterns may help improve our ability to link genes, brains, and behavior by identifying reliable and reproducible endophenotypes. Work using connectivity-based predictive modeling has generated brain-based proxies of behavioral and neuropsychological variables. If such models capture activity in inherited brain systems, they may offer a more powerful link between genes and behavior.

Method

As a proof of concept, we develop models predicting intelligence (IQ) based on fMRI connectivity and test their effectiveness as endophenotypes. We link brain and IQ in a model development dataset of N = 3,000 individuals and test the genetic correlations between brain models and measured IQ in a genetic validation sample of N = 13,092 individuals from the UK Biobank. We compare an additive connectivity-based model to multivariate LASSO and ridge models phenotypically and genetically. We also compare these approaches to single "candidate" brain areas.

Results

We found that predictive brain models were significantly phenotypically correlated with IQ and showed much stronger correlations than individual edges. Further, brain models were more heritable (h2 = 0.155-0.181) than single brain regions (h2 = 0.038-0.118) and captured about half of the genetic variance in IQ (rG = 0.422-0.576), while rGs with single brain measures were smaller and nonsignificant. For the different approaches, LASSO and ridge were similarly predictive, with slightly weaker performance of the additive model. LASSO model weights were highly theoretically interpretable and replicated known brain IQ associations. Finally, functional connectivity models trained in midlife showed genetic correlations with early life correlates of IQ, suggesting some stability in the prediction of fMRI models.

Conclusion

Multisystem predictive models hold promise as imaging endophenotypes that offer complex and theoretically relevant conclusions for future imaging genetics research.