Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity

Abstract

Klinefelter syndrome (KS) (47,XXY) is the most common male sex chromosome aneuploidy. Diagnosis and clinical supervision remain a challenge due to varying phenotypic presentation and insufficient characterization of the syndrome. Here we combine health data-driven epidemiology and molecular level systems biology to improve the understanding of KS and the molecular interplay influencing its comorbidities. In total, 78 overrepresented KS comorbidities were identified using in- and out-patient registry data from the entire Danish population covering 6.8 million individuals. The comorbidities extracted included both clinically well-known (e.g. infertility and osteoporosis) and still less established KS comorbidities (e.g. pituitary gland hypofunction and dental caries). Several systems biology approaches were applied to identify key molecular players underlying KS comorbidities: Identification of co-expressed modules as well as central hubs and gene dosage perturbed protein complexes in a KS comorbidity network build from known disease proteins and their protein-protein interactions. The systems biology approaches together pointed to novel aspects of KS disease phenotypes including perturbed Jak-STAT pathway, dysregulated genes important for disturbed immune system (IL4), energy balance (POMC and LEP) and erythropoietin signalling in KS. We present an extended epidemiological study that links KS comorbidities to the molecular level and identify potential causal players in the disease biology underlying the identified comorbidities.

Figure 1

Klinefelter syndrome (KS) comorbidities extracted from Danish patient records (n = 78). Comorbidities are summarised by disease chapter and each dot represents a KS comorbidity with a certain relative risk (RR). The disease chapter titles are shortened (see Supplementary Material, Table S2). There were no comorbidities between KS and disorders from chapters 2, 7, 8, 16 and 18–21. See Supplementary Material, Table S1 for the full list of KS comorbidities and RRs.

Figure 2

Gene co-expression modules correlating with Klinefelter syndrome (KS) status. (A) Gene co-expression analysis dendrogram showing co-expressed gene modules identified using Weighted gene co-expression network analysis (WGCNA) (n = 54). The top colour bar states expression correlation with KS status (red: positive correlation; blue: negative correlation). The bar below informs about module membership. In total, 27 modules correlated significantly with KS status and reported here as coloured across the dendrogram. (B) Scaled expression per individual of the 99 genes in the most positively correlated module with KS status, M1/saddlebrown. (C) Scaled expression per individual of the 81 genes in the most negatively correlated module with KS status, M2/skyblue3.

Figure 3

Klinefelter syndrome (KS) comorbidity network, disease separation and protein complex with disturbed functionality. (A) The global KS comorbidity network created from disease-associated proteins from knowledge databases linked by observed protein–protein interactions (PPIs). The network represents the sub-networks for KS and the 22 comorbidities with significant high connectivity. Nodes are coloured according to their associated disease chapter similarly to Figure 1. Nodes associated to diseases belonging to multiple chapters are multi-coloured. Node size is scaled to the number of KS comorbidities each node is associated with. (B) Disease separations of the 23 diseases represented in the comorbidity network clustered after similarity and only including edges between diseases with overlapping network topology. (C) The most statistical significant cluster in the network. The size and colouring of the nodes are similar to in the full network. Node border colour represents significant up- (red) and down-regulation (blue) in KS compared to controls.