Underestimated Aspect of Mucopolysaccharidosis Pathogenesis: Global Changes in Cellular Processes Revealed by Transcriptomic Studies

Abstract

Mucopolysaccharidoses (MPS), a group of inherited metabolic disorders caused by deficiency in enzymes involved in degradation of glycosaminoglycans (GAGs), are examples (and models) of monogenic diseases. Accumulation of undegraded GAGs in lysosomes was supposed to be the major cause of MPS symptoms; however, their complexity and variability between particular types of the disease can be hardly explained by such a simple storage mechanism. Here we show that transcriptomic (RNA-seq) analysis of the material derived from fibroblasts of patients suffering from all types and subtypes of MPS, supported by RT-qPCR results, revealed surprisingly large changes in expression of genes involved in various cellular processes, indicating complex mechanisms of MPS. Although each MPS type and subtype was characterized by specific changes in gene expression profile, there were genes with significantly changed expression relative to wild-type cells that could be classified as common for various MPS types, suggesting similar disturbances in cellular processes. Therefore, both common features of all MPS types, and differences between them, might be potentially explained on the basis of changes in certain cellular processes arising from disturbed regulations of genes' expression. These results may shed a new light on the mechanisms of genetic diseases, indicating how a single mutation can result in complex pathomechanism, due to perturbations in the network of cellular reactions. Moreover, they should be considered in studies on development of novel therapies, suggesting also why currently available treatment methods fail to correct all/most symptoms of MPS. We propose a hypothesis that disturbances in some cellular processes cannot be corrected by simple reduction of GAG levels; thus, combined therapies are necessary which may require improvement of these processes.

Keywords: cellular processes; mucopolysaccharidoses; transcriptomic analyses.

Figure 1

Number of up- and down-regulated transcripts (at FDR < 0.1; p < 0.1) in different types of MPS relative to control cells (HDFa).

Figure 2

Number of up- and down-regulated transcripts (at FDR < 0.1; p < 0.1) with division into selected cellular processes in different MPS types relative to control cells (HDFa).

Figure 3

Cellular processes in which at least 30 kinds of transcripts were particularly strongly changed (FDR < 10⁻⁶, p < 0.1) in different MPS types. The “rainbow” diagram (A) shows these processes in order to demonstrate which process in significantly affected in which MPS types. The colors correspond to MPS types shown in panel (B), in which the number of severely changed transcripts of genes which products are involved in particular processes are indicated.

Figure 4

Chord diagrams indicating numbers of common genes between individual MPS types for which expression is particularly strongly changed (FDR < 10⁻⁶, p < 0.1) relative to control cell (HDFa line). Individual panels group genes involved in indicated cellular processes. Roman numbers indicate corresponding MPS types.

Figure 5

Comparison of results of RNA-seq (blue columns) and RT-qPCR (red columns) for selected genes in various MPS types relative to wild-type HDFa cells. Results for HDFa are normalized as a horizontal line (value 0), and values for particular MPS types reflect this value, with changes in transcript level indicated as log₂ fold change (FC). Results are presented as mean values from four biological experiments, with error bars indicating SD. In all cases, the differences between MPS cells and HDFa cells were statistically significant (p < 0.05 in one-way ANOVA). Particular genes were tested in different MPS types, as follows: CLU in MPS II, HIP1 in MPS IIIB, ATF5 in MPS IX, COL5A1 in MPS IIIC, MFGE8 in MPS IIIA, SCARA3 in MPS VI, STS in MPS IIID, and MAN2A in MPS VII.