Fig 1: Knockdown of exosc9 in Zebrafish Causes Abnormal Neuromuscular Development(A) Whole-mount immunofluorescence of the pan-neuronal marker HuC shows that the midbrain (∗) appears abnormal and the cerebellum (#) and hindbrain (+) are absent in representative exosc9 morphants and crispants compared with uninjected controls.(B) Islet1:GFP transgenic morphant and crispant zebrafish have absent cranial posterior nerve V (Vp).(C) Whole-mount immunofluorescence of synaptic vesicle 2 (SV2, motorneurons, green) and α-bungarotoxin (neuromuscular junctions, red) shows that motoneurons and neuromuscular junctions failed to properly develop in exosc9 morphants and crispants compared with uninjected controls (white arrows).(D) Phalloidin staining shows that muscle failed to develop properly. Fibers were sparser, more spread out, and irregular in the exosc9 morphants and crispants. All experiments were performed in 48 hpf zebrafish.
Fig 2: Strategies Targeting exosc9 in Zebrafish(A) Schematic of exosc9 in zebrafish demonstrating the sites to where the morpholino, gRNA, and primers were targeted.(B) RT-PCR of zebrafish morphants. The morpholino caused the retention of an intron and a reduction of the WT product in a dose-dependent fashion. The identity of the bands was confirmed by Sanger sequencing.(C) The target sequence for exosc9 gRNA and an example of a mutation found in a crispant.(D) The mutation rate found in crispants of differing phenotypes.
Fig 3: RNA-Seq and qPCR in Fibroblasts of Affected Individual 1:II-1 Carrying the Homozygous c.41T>C Sequence Variant in EXOSC9(A) Differential expression analysis (DESeq2) detected 69 genes that were significantly upregulated and 138 that were significantly downregulated in the affected individuals’ fibroblasts.(B) Gene-set enrichment analysis of GO terms with differentially expressed genes in fibroblast RNA-seq.(C) Comparison of the numbers of upregulated and downregulated genes in muscle biopsy specimens of RNA-seq between affected individual 1:II-1 and affected individual 2:II-1. 2,778 transcripts were upregulated in both affected individuals, whereas 2,864 transcripts were downregulated in both. 18 transcripts that were upregulated in affected individual 2:II-1 were downregulated in affected individual 1:II-1, and 45 transcripts were upregulated in affected individual 1:II-1 but downregulated in affected individual 2:II-1.(D) Gene expression analysis of HOXC6, HOXC8, HOXC9, and HOTAIR through qRT-PCR in EXOSC3, EXOSC8, EXOSC9, and RBM7 mutant fibroblasts. Results were normalized to the average values obtained from two control fibroblast lines.
Fig 4: Clinical Presentation and Pedigrees(A) Clinical photos of affected individual 1:II-1. She had multiple joint contractures. Hands were fisted with thumbs adducted, and feet were maintained in an extended cavo-varus position.(B) Segregation of the EXOSC9 sequence variants in the four pedigrees.(C) Electropherograms of the EXOSC9 sequence variants identified in this study.
Fig 5: The Exosome Complex Is Reduced in Affected Individuals’ Fibroblasts(A) Immunoblotting of fibroblasts from affected individuals with variants in different components of the exosome complex (the homozygous c.92G>C in EXOSC3, the homozygous c.5C>T in EXOSC8, the homozygous c.41T>C in EXOSC9 [individual 1:II-1], and the homozygous c.236C>G in RBM7) shows reduced EXOSC9, but other components of the exosome complex were also reduced. Actin was used as a loading control.(B) Blue native polyacrylamide gel electrophoresis (BN-PAGE) shows that there is a reduction of the assembly of the whole exosome complex in affected individuals’ fibroblasts. GAPDH was used as a loading control.(C) Immunoblot on muscle extracts from affected individual 2:II-1 and four controls confirms that EXOSC9 was severely reduced in affected individual 2:II-1.
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