1
|
Moodie JE, Harris SE, Harris MA, Buchanan CR, Davies G, Taylor A, Redmond P, Liewald DCM, Valdés Hernández MDC, Shenkin S, Russ TC, Muñoz Maniega S, Luciano M, Corley J, Stolicyn A, Shen X, Steele D, Waiter G, Sandu A, Bastin ME, Wardlaw JM, McIntosh A, Whalley H, Tucker‐Drob EM, Deary IJ, Cox SR. General and specific patterns of cortical gene expression as spatial correlates of complex cognitive functioning. Hum Brain Mapp 2024; 45:e26641. [PMID: 38488470 PMCID: PMC10941541 DOI: 10.1002/hbm.26641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/29/2024] [Accepted: 02/18/2024] [Indexed: 03/18/2024] Open
Abstract
Gene expression varies across the brain. This spatial patterning denotes specialised support for particular brain functions. However, the way that a given gene's expression fluctuates across the brain may be governed by general rules. Quantifying patterns of spatial covariation across genes would offer insights into the molecular characteristics of brain areas supporting, for example, complex cognitive functions. Here, we use principal component analysis to separate general and unique gene regulatory associations with cortical substrates of cognition. We find that the region-to-region variation in cortical expression profiles of 8235 genes covaries across two major principal components: gene ontology analysis suggests these dimensions are characterised by downregulation and upregulation of cell-signalling/modification and transcription factors. We validate these patterns out-of-sample and across different data processing choices. Brain regions more strongly implicated in general cognitive functioning (g; 3 cohorts, total meta-analytic N = 39,519) tend to be more balanced between downregulation and upregulation of both major components (indicated by regional component scores). We then identify a further 29 genes as candidate cortical spatial correlates of g, beyond the patterning of the two major components (|β| range = 0.18 to 0.53). Many of these genes have been previously associated with clinical neurodegenerative and psychiatric disorders, or with other health-related phenotypes. The results provide insights into the cortical organisation of gene expression and its association with individual differences in cognitive functioning.
Collapse
Affiliation(s)
- Joanna E. Moodie
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
| | - Sarah E. Harris
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
| | - Mathew A. Harris
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
| | - Colin R. Buchanan
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
| | - Gail Davies
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
| | - Adele Taylor
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
| | - Paul Redmond
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
| | - David C. M. Liewald
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
| | - Maria del C. Valdés Hernández
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
- Centre for Clinical Brain SciencesUniversity of EdinburghUK
| | - Susan Shenkin
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
- Centre for Clinical Brain SciencesUniversity of EdinburghUK
- Ageing and Health Research Group, Usher InstituteUniversity of EdinburghUK
| | - Tom C. Russ
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
- Centre for Clinical Brain SciencesUniversity of EdinburghUK
- Alzheimer Scotland Dementia Research CentreUniversity of EdinburghUK
| | - Susana Muñoz Maniega
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
- Centre for Clinical Brain SciencesUniversity of EdinburghUK
| | - Michelle Luciano
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
| | - Janie Corley
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
| | - Aleks Stolicyn
- Centre for Clinical Brain SciencesUniversity of EdinburghUK
| | - Xueyi Shen
- Centre for Clinical Brain SciencesUniversity of EdinburghUK
| | - Douglas Steele
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
| | - Gordon Waiter
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
| | - Anca‐Larisa Sandu
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
| | - Mark E. Bastin
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
- Centre for Clinical Brain SciencesUniversity of EdinburghUK
| | - Joanna M. Wardlaw
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
- Centre for Clinical Brain SciencesUniversity of EdinburghUK
| | | | | | | | - Ian J. Deary
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
| | - Simon R. Cox
- Lothian Birth Cohorts, Department of PsychologyThe University of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) CollaborationEdinburghUK
| |
Collapse
|
2
|
Yeung HW, Stolicyn A, Buchanan CR, Tucker‐Drob EM, Bastin ME, Luz S, McIntosh AM, Whalley HC, Cox SR, Smith K. Predicting sex, age, general cognition and mental health with machine learning on brain structural connectomes. Hum Brain Mapp 2023; 44:1913-1933. [PMID: 36541441 PMCID: PMC9980898 DOI: 10.1002/hbm.26182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 11/11/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
There is an increasing expectation that advanced, computationally expensive machine learning (ML) techniques, when applied to large population-wide neuroimaging datasets, will help to uncover key differences in the human brain in health and disease. We take a comprehensive approach to explore how multiple aspects of brain structural connectivity can predict sex, age, general cognitive function and general psychopathology, testing different ML algorithms from deep learning (DL) model (BrainNetCNN) to classical ML methods. We modelled N = 8183 structural connectomes from UK Biobank using six different structural network weightings obtained from diffusion MRI. Streamline count generally provided the highest prediction accuracies in all prediction tasks. DL did not improve on prediction accuracies from simpler linear models. Further, high correlations between gradient attribution coefficients from DL and model coefficients from linear models suggested the models ranked the importance of features in similar ways, which indirectly suggested the similarity in models' strategies for making predictive decision to some extent. This highlights that model complexity is unlikely to improve detection of associations between structural connectomes and complex phenotypes with the current sample size.
Collapse
Affiliation(s)
- Hon Wah Yeung
- Department of PsychiatryUniversity of EdinburghEdinburghUK
| | - Aleks Stolicyn
- Department of PsychiatryUniversity of EdinburghEdinburghUK
| | - Colin R. Buchanan
- Department of PsychologyUniversity of EdinburghEdinburghUK
- Lothian Birth Cohorts, University of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence Collaboration (SINAPSE)EdinburghUK
| | - Elliot M. Tucker‐Drob
- Department of PsychologyUniversity of TexasAustinTexasUSA
- Population Research Center and Center on Aging and Population SciencesUniversity of Texas at AustinAustinTexasUSA
| | - Mark E. Bastin
- Lothian Birth Cohorts, University of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence Collaboration (SINAPSE)EdinburghUK
- Centre for Clinical Brain ScienceUniversity of EdinburghEdinburghUK
| | - Saturnino Luz
- Edinburgh Medical SchoolUsher Institute, The University of EdinburghEdinburghUK
| | - Andrew M. McIntosh
- Department of PsychiatryUniversity of EdinburghEdinburghUK
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular Medicine, University of EdinburghEdinburghUK
| | | | - Simon R. Cox
- Department of PsychologyUniversity of EdinburghEdinburghUK
- Lothian Birth Cohorts, University of EdinburghEdinburghUK
- Scottish Imaging Network, A Platform for Scientific Excellence Collaboration (SINAPSE)EdinburghUK
| | - Keith Smith
- Department of Physics and MathematicsNottingham Trent UniversityNottinghamUK
| |
Collapse
|