Exome reanalysis and proteomic profiling identified TRIP4 as a novel cause of cerebellar hypoplasia and spinal muscular atrophy (PCH1)

Abstract

TRIP4 is one of the subunits of the transcriptional coregulator ASC-1, a ribonucleoprotein complex that participates in transcriptional coactivation and RNA processing events. Recessive variants in the TRIP4 gene have been associated with spinal muscular atrophy with bone fractures as well as a severe form of congenital muscular dystrophy. Here we present the diagnostic journey of a patient with cerebellar hypoplasia and spinal muscular atrophy (PCH1) and congenital bone fractures. Initial exome sequencing analysis revealed no candidate variants. Reanalysis of the exome data by inclusion in the Solve-RD project resulted in the identification of a homozygous stop-gain variant in the TRIP4 gene, previously reported as disease-causing. This highlights the importance of analysis reiteration and improved and updated bioinformatic pipelines. Proteomic profile of the patient's fibroblasts showed altered RNA-processing and impaired exosome activity supporting the pathogenicity of the detected variant. In addition, we identified a novel genetic form of PCH1, further strengthening the link of this characteristic phenotype with altered RNA metabolism.

Fig. 1. Magnetic resonance imaging (MRI).

Cranial and thoracic MRI performed at the age of 6 weeks revealed a hypoplastic cerebellum, necrosis and haemorrhage of the occipital cortex, pronounced atrophy of skeletal musculature and confirmed bilateral pleural effusion.

Fig. 2. In silico studies of proteomic data.

Gene Ontology (GO) term analysis was performed focussing on the up- and downregulated proteins separately: (A) “Biological Processes”revealed that the majority of increased proteins is involved in RNA processing, whereas most of decreased proteins (B) control the response to oxidative stress or are involved in protein folding. “Molecular Function” revealed that proteins involved in RNA-binding and modulating nucleotide binding are increased (C), and those involved in the cytoskeleton structure and the modulation of oxidative stress predominate amongst the downregulated (D). “Cellular Component” showed that the proteins upregulated in the patient-derived fibroblasts mostly belong to the nucleus (E) and the ER, the lysosome, mitochondria, and the cytoskeleton are downregulated (F). The proteomaps-based pathway analysis also focussed on increased and decreased proteins separately. G For increased proteins, it confirmed changes in RNA-transport and RNA-processing, and indicated an activation of the protein clearance machinery (Ubiquitin-mediated proteolysis via the proteasome) as well as altered signalling processes (Ras, ErbB and MAPK pathways). H For decreased proteins, indicated a vulnerability of cellular metabolism accompanied by perturbed signalling cascades (Jak-STAT, ErbB, MAPK, PI3K-AKT & NF-kappa-B pathways) and reduced lysosomal as well as exosome function.