Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas

Abstract

Migraine is a common disabling neurovascular brain disorder typically characterised by attacks of severe headache and associated with autonomic and neurological symptoms. Migraine is caused by an interplay of genetic and environmental factors. Genome-wide association studies (GWAS) have identified over a dozen genetic loci associated with migraine. Here, we integrated migraine GWAS data with high-resolution spatial gene expression data of normal adult brains from the Allen Human Brain Atlas to identify specific brain regions and molecular pathways that are possibly involved in migraine pathophysiology. To this end, we used two complementary methods. In GWAS data from 23,285 migraine cases and 95,425 controls, we first studied modules of co-expressed genes that were calculated based on human brain expression data for enrichment of genes that showed association with migraine. Enrichment of a migraine GWAS signal was found for five modules that suggest involvement in migraine pathophysiology of: (i) neurotransmission, protein catabolism and mitochondria in the cortex; (ii) transcription regulation in the cortex and cerebellum; and (iii) oligodendrocytes and mitochondria in subcortical areas. Second, we used the high-confidence genes from the migraine GWAS as a basis to construct local migraine-related co-expression gene networks. Signatures of all brain regions and pathways that were prominent in the first method also surfaced in the second method, thus providing support that these brain regions and pathways are indeed involved in migraine pathophysiology.

Fig. 1

Gene expression patterns and cell type enrichments of the 18 modules in the spatial co-expression network. a Heat map of the clustered gene expression data, with the 3702 concatenated human brain samples in columns and the 19,972 genes in rows, ordered according to their clustering. The brain samples are ordered based on their location in the brain, which is noted above the heat map and illustrated with the colour coding from the Allen Brain Institute below the heat map. The colour coding is also illustrated in the three coronal brain sections below the heat map (for brain region names in the coronal sections, see Figure S3). Low expression is shown as blue, high expression is shown as red. The genes are clustered into 18 modules, here separated by white rows. b Log-transformed gene-based P values for the association with migraine are shown for all genes with: (1) genes with P values below 0.05 in the colour corresponding to modules A–E or in grey for the other modules; (2) migraine candidate genes in black; and (3) high-confidence genes circled and named. Gene modules A–E are the five modules enriched for candidate genes. c the table shows the enrichment of cell type-specific genes in the 18 modules from white (P value >0.05) to black (P value <10⁻⁷)

Fig. 2

Gene expression maps for modules A–E associated with migraine. Average gene expression levels are shown for each module from blue (low) to red (high) in the different brain regions represented in the three coronal brain sections (for brain region names in the coronal sections, see Figure S3). Regions that lack gene expression information are depicted in grey. The lists on the right show: (1) the numbers of genes and migraine candidate genes; (2) the P values for the enrichment of migraine candidate genes; and (3) the top 5 enriched functions in each module, as identified using the Functional Annotation Clustering tool in DAVID, with their corresponding EASE score. The EASE score is the geometric mean of the Benjamini-corrected negative log (base 10) P values of its pathways and GO terms, so a score below 1.3 corresponds to a Benjamini-corrected P value below 0.05. Module E has no significant functional enrichments

Fig. 3

Gene co-expression network seeded on the 14 high-confidence genes. a The network consists of the high-confidence genes and their co-expression partners that are connected if they have a co-expression value >0.6. Each gene is shown as a circle and named with its gene name, with the size of both corresponding to its gene-based P value (larger size corresponding to a lower P value). The colours of the circles correspond to those of modules A–E in Fig. 1: blue for module A, yellow for module B, green for module C, red for module D, purple for module E and grey for all other modules. The edge colours are matched to (a mixture of) the colours of the connecting genes. b For each high-confidence gene and its co-expressing partners are shown: (1) the number of genes in the local co-expression network around the high-confidence gene; (2) the average brain gene expression level from blue (low expression) to red (high expression) mapped in the three coronal brain sections (for brain region names in the coronal sections, see Figure S3); (3) the enrichment of cell type-specific genes in the table from white (P value >0.05) to black (P value <10⁻⁷); and (4) the top five enriched gene functions. Not shown are boxes for high-confidence genes TRPM8, SUV39H2 and FHL5 because these genes have no or only few co-expressed genes. Ne. Neuron, As. astrocyte, Ol. Oligodendrocyte, Mi. microglia, En. endothelial cell

Fig. 4

Schematic overview of the migraine-associated modules and the trigeminovascular pathway involved in migraine headache. The migraine-associated modules A–D, which also overlap with the local migraine-related co-expression gene network, point to three distinct locations in the brain: the cortex (modules A, B and C), the cerebellum (module B) and the white matter and subcortical regions including the thalamus (module D), and multiple gene functions or cell types. Several brain regions overlap between the migraine-associated modules and the trigeminovascular system that is thought to generate the migraine headache. This system consists of trigeminal afferents that innervate the blood vessels in the meninges, whose signals are transmitted through the trigeminal ganglion (TG), the trigeminal nucleus caudalis (TNC), and the thalamus to the cortex where they can produce the sensation of pain