Convergent transcriptomic and neuroimaging signature of Autism Spectrum Disorder

TL;DR

This study integrates neuroimaging and transcriptomics data to identify a reliable biomarker for Autism Spectrum Disorder, demonstrating a deep learning classifier and gene modules linked to ASD brain regions.

Contribution

It introduces a confounder-resilient deep learning classifier for ASD using MRI data and links neuroimaging signatures with gene expression modules, advancing biomarker discovery.

Findings

Deep learning classifier achieved AUC of 0.89 on independent test set.

Identified five gene network modules involved in ASD.

Linked neuroimaging features with high expression of four gene modules.

Abstract

Autism Spectrum Disorder (ASD) is a multi-factorial neurodevelopmental disorder, whose causes are still poorly understood. Effective therapies to reduce all the heterogeneous symptoms of the disorder do not exists yet, but behavioural programs started at a very young age may improve the quality of life of the patients. For this reason, many efforts have been dedicated to the research of a reliable biomarker for early diagnosis. Machine learning approaches to distinguish ASDs from healthy controls based on their brain Magnetic Resonance Images (MRIs) have been plagued by the problem of confounders, showing poor classification performance and inconsistency in the biomarker definition. Brain transcriptomics studies, instead, showed some converging results, but being based on data that can be acquired only post-mortem they are not useful for diagnosis. In this work, using an imaging transcriptomics approach, the following results have been obtained. 1) A deep learning based classifier resilient to confounders and able to exploit the temporal dimension of resting state functional MRIs has been developed, reaching an AUC of 0.89 on an independent test set. 2) Five gene network modules involved in ASD have been identified, by analyzing brain transcriptomics data of subjects with ASD and healthy controls. 3) By comparing the brain regions relevant for the classifier obtained in the first step and the brain-wide gene expression profiles of the modules of interest obtained in the second step, it has been proved that the regions that characterize ASD brain at the neuroimaging level are those in which four out of the five gene modules take a significantly high absolute value of expression. These results prove that, despite the heterogeneity of the disorder, it is possible to identify a neuroimaging-based biomarker of ASD, confirmed by transcriptomics.