Whole organism transcriptome analysis of zebrafish models of Bardet-Biedl Syndrome and Alström Syndrome provides mechanistic insight into shared and divergent phenotypes

Abstract

Background: Bardet-Biedl Syndrome (BBS) and Alström Syndrome are two pleiotropic ciliopathies with significant phenotypic overlap between them across many tissues. Although BBS and Alström genes are necessary for the proper function of primary cilia, their role in defects across multiple organ systems is unclear.

Methods: To provide insight into the pathways underlying BBS and Alström phenotypes, we carried out whole organism transcriptome analysis by RNA sequencing in established zebrafish models of the syndromes.

Results: We analyzed all genes that were significantly differentially expressed and found enrichment of phenotypically significant pathways in both models. These included multiple pathways shared between the two disease models as well as those unique to each model. Notably, we identified significant downregulation of genes in pathways relevant to visual system deficits and obesity in both disorders, consistent with those shared phenotypes. In contrast, neuronal pathways were significantly downregulated only in the BBS model but not in the Alström model. Our observations also suggested an important role for G-protein couple receptor and calcium signaling defects in both models.

Discussion: Pathway network analyses of both models indicate that visual system defects may be driven by genetic mechanisms independent of other phenotypes whereas the majority of other phenotypes are a result of genetic players that contribute to multiple pathways simultaneously. Additionally, examination of genes differentially expressed in opposing directions between the two models suggest a deficit in pancreatic function in the Alström model, that is not present in the BBS model.

Conclusions: These findings provide important novel insight into shared and divergent phenotypes between two similar but distinct genetic syndromes.

Fig. 1

Differentially expressed genes in BBS and Alström models. Numbers of genes upregulated (red) or downregulated (yellow) in alms1 MO (green) injected embryos, bbs1 MO (orange) injected embryos or both compared to standard control MO injected embryos. * Denotes number of genes changed in both but having opposite changes in expression

Fig. 2

Top up- and downregulated pathways and enriched GO terms in BBS model. a Top 30 downregulated pathways by number of genes. b Top 30 downregulated GO terms by fold enrichment. c Top 30 upregulated pathways by number of genes. d Top upregulated GO terms by fold enrichment

Fig. 3

Top up- and downregulated pathways and enriched GO terms in Alström model. a Top downregulated pathways by number of genes. b Top downregulated GO terms by fold enrichment. c Top upregulated pathways by number of genes

Fig. 4

Overlap of differential expression between BBS and Alström models. a Percentage and number of differentially expressed genes found unique to each disease model (red) and shared across both models (blue). b Downregulated pathways by number of genes downregulated in both models. c Downregulated GO terms by fold enrichment of genes downregulated in both models. Number of genes or GO terms downregulated in the BBS model (green), in the Alström model (red) or both (blue) indicated

Fig. 5

Pathway networks of overlapping genes in BBS and Alström models. Pathway analysis of top 30 downregulated pathways among differentially expressed genes in BBS model (a) or in Alström model (b). c Pathway connectivity of downregulated pathways found in both models. Pathway connections determined by a minimum of 20 % shared genes between pathways and at least 2 genes overlap

Fig. 6

Top downregulated pathways and enriched GO terms unique to the BBS model. a Top 30 downregulated pathways by number of genes only differentially expressed in the BBS model. b Top 30 downregulated GO terms by fold enrichment of genes only differentially expressed in the BBS model

Fig. 7

Genes differentially expressed in opposing directions between BBS and Alström models. a Log fold change (LFC) of genes differentially expressed in opposite directions between both disease models. b Table showing gene names, LFC relative to controls, p-values relative to controls, and false discovery rates (FDR) for 8 genes showing opposing changes in differential expression among BBS and Alström models

Fig. 8

Summary of pathway and GO term analysis results. a Pathway analysis summary of upregulated and downregulated enriched pathways found in the BBS model (red), the Alström model (blue) or both. b Gene Ontology (GO) term analysis summary of upregulated and downregulated enriched GO terms found in the BBS model (red), the Alström model (blue) or both