Polygenic disruption of retinoid signalling in schizophrenia and a severe cognitive deficit subtype

Abstract

Retinoid metabolites of vitamin A are intrinsically linked to neural development, connectivity and plasticity, and have been implicated in the pathophysiology of schizophrenia. We hypothesised that a greater burden of common and rare genomic variation in genes involved with retinoid biogenesis and signalling could be associated with schizophrenia and its cognitive symptoms. Common variants associated with schizophrenia in the largest genome-wide association study were aggregated in retinoid genes and used to formulate a polygenic risk score (PRS_Ret) for each participant in the Australian Schizophrenia Research Bank. In support of our hypothesis, we found PRS_Ret to be significantly associated with the disorder. Cases with severe cognitive deficits, while not further differentiated by PRS_Ret, were enriched with rare variation in the retinoic acid receptor beta gene RARB, detected through whole-genome sequencing. RARB rare variant burden was also associated with reduced cerebellar volume in the cases with marked cognitive deficit, and with covariation in grey matter throughout the brain. An excess of rare variation was further observed in schizophrenia in retinoic acid response elements proximal to target genes, which we show are differentially expressed in the disorder in two RNA sequencing datasets. Our results suggest that genomic variation may disrupt retinoid signalling in schizophrenia, with particular significance for cases with severe cognitive impairment.

Fig. 1

Overview of investigation of the impact of common and rare variation in retinoid genes. Using gene ontology and the wider literature, a panel of 107 genes involved with retinoid biology were collated and tested for the aggregated effect of GWAS SNPs using MAGMA. An uncorrected threshold of P < 0.05 was used to delineate genes with evidence of a polygenic effect. Polygenic risk score (PRS) was then calculated in individuals for this retinoid panel. Retinoid PRS was associated with schizophrenia but did not disproportionately affect the cognitive deficit (CD) subtype. Rare variant association (MAF < 0.01%) from whole-genome sequencing was tested at gene level for each of the 22 genes using the SKAT-O framework. The retinoic acid receptor gene RARB was significantly associated with the CD population, but there were no significant gene level signals for the full case cohort (cognitively mixed) relative to controls

Fig. 2

GWAS variant enrichment in retinoid genes and their relative tissue specificity. a Enrichment of schizophrenia GWAS variants in retinoid genes, genes highlighted blue are below the threshold of nominal uncorrected significance (P < 0.05). b Tissue-specific expression of 22 significant MAGMA genes relative to the rest of the retinoid panel. Bars highlighted red are statistically significant after multiple testing correction. One-sided (for upregulation and downregulation) and two-sided tests are reported. DEG = differentially expressed genes. c Distribution of retinoid polygenic risk score (PRS_Ret), constructed using the most significantly associated P-value threshold, in the schizophrenia and healthy control cohorts. The black line represents the population mean for controls (left) and cases (right)

Fig. 3

Rare variants in the retinoid receptor gene RARB enriched in a severe cognitive subtype of schizophrenia. a The combined effect of rare variants was tested at gene level using the SKAT-O test; analyses comparing cases with controls, and directly comparing cognitively spared [CS] with cognitive deficit [CD] cases of schizophrenia were conducted. Blue Bonferroni threshold corrected for the 22 genes tested for two phenotypes. b, c Expression of RARB in different brain regions from BrainSpan at (b) 13–15 weeks post conception (pcw) and (c) 6–18 months (mos) post-natal development. STC = caudal superior temporal cortex, A1C = primary auditory cortex, IPC = inferior parietal cortex, S1C = primary somatosensory cortex, M1C = primary motor cortex, DFC = dorsolateral prefrontal cortex, VFC = ventrolateral prefrontal cortex, OFC = orbital frontal cortex, ITC  =inferior temporal cortex, V1C = primary visual cortex, STR = striatum, MFC = medial prefrontal cortex, OFC = orbital frontal cortex, AMY = amygdala, HIP = hippocampus, CB = cerebellum

Fig. 4

Association between RARB rare variant burden and neurophysiological phenotypes. a Interaction between RARB rare variant burden and volume (right) of a voxel cluster in the exterior of the left posterior cerebellum (left). Red points indicate the cognitive deficit (CD) subtype, whereas blue points represent cognitively spared (CS) schizophrenia cases. Coordinates of the significant cluster with reduced volume after voxel-wise correction (x, y and z) are stated. b Inter-subject covariance of grey matter significantly predicted by RARB rare variant burden in CD patients in regions outside the cerebellum. Source-based morphometry identified components (spatial regions) in which the covariation of grey matter concentration (GMC) was interrelated between individuals. Z-value indicates correlation between subjects, with a positive Z-value representing positively correlated inter-subject covariation and vice versa. Component C23: orange positive z-value region – precuneus, postcentral gyrus, paracentral lobule, sub-gyral, superior parietal lobule, inferior parietal lobule, medial frontal gyrus; blue negative z-value region – middle temporal ggyrus, inferior occipital gyrus. Component C8: orange positive z-value region – precuneus, sub-gyral, cuneus, superior parietal lobule; blue negative z-value region – middle temporal gyrus, angular gyrus, superior temporal gyrus