Dataset Information

Structural and functional analysis of the novel pathological variant c.1024G>A in the SIL1 gene causing Marinesco-Sjögren syndrome

ABSTRACT: Marinesco-Sjögren syndrome (MSS) is a rare autosomal recessive neuromuscular disease. MSS patients suffer from ataxia, muscle weakness and cataracts; mental retardation and skeletal abnormalities are often present. In many cases the syndrome is caused by loss of function variant in the SIL1 gene, which encodes for an endoplasmic reticulum-localised BiP nucleotide exchange factor. The loss of Sil1 impairs BiP functions, which in turn leads to the accumulation of unfolded proteins and thus activation of unfolded protein response (UPR). This response most likely participates in the degeneration of Purkinje neurons and myopathy. Different SIL1 variants were reported so far, but a clear relationship with the phenotype was not established. We examined a 2-year-old patient presenting with ataxia, muscle weakness, and cataracts, the classic triad used to make a clinical diagnosis of MSS. Whole exome sequencing revealed a previously undescribed c.1024G>A variant in the SIL1 gene. Multiple in-silico analysis suggested that this variant of unknown significance (VUS) is likely pathogenic. The disruption of the three-dimensional organisation of the recombinant mutant protein (p.E342K) was revealed by circular dichroism and native gel electrophoresis. Primary skin fibroblasts isolated from the patient carrying the new SIL1 variant showed ten times less Sil1 protein than healthy control fibroblasts, most likely because the protein is misfolded and thus degraded. In fact, inhibition of proteasome activity increased the amount of Sil1 protein. Proteomic analysis of these fibroblasts revealed a typical protein expression pattern and ontologies enrichment resembling that of an MSS patient carrying the R111X variant and the Sil1Gt mouse model of MSS. In addition, these fibroblasts showed a transcription signature characteristic of MSS. Finally, ultrastructural analysis revealed the presence of autophagic vacuoles and accumulation of lipid droplets mirroring the features seen in fibroblasts from a patient with a declared MSS. Overall, these evidences support the hypothesis that the novel p.E342K variant is pathological and thus explain the clinical manifestation observed in the patientcarrying this variant.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Fibroblast

DISEASE(S): Sjogren's Syndrome

SUBMITTER: Federica Di Marco

LAB HEAD: Michele Sallese

PROVIDER: PXD062620 | Pride | 2025-12-22

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20230724_HF_CRTR_01_2ul.raw	Raw
	20230724_HF_CRTR_02.raw	Raw
	20230724_HF_CRTR_03.raw	Raw
	20230724_SIL1_GRECIA_01.raw	Raw
	20230724_SIL1_GRECIA_02.raw	Raw

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Publications

A Novel <i>SIL1</i> Variant (p.E342K) Associated with Marinesco-Sjögren Syndrome Impairs Protein Stability and Function.

Ruggieri Anna Giulia AG Marinakis Nikolaos M NM Amodei Laura L Potenza Francesca F Kampouraki Afrodite A Tilemis Faidon-Nikolaos FN Pietrangelo Laura L Viele Marianna M Di Marco Federica F Del Boccio Piero P Di Cintio Federica F Selenti Nikoletta N Valari Manthoula M Federici Luca L Miele Adriana Erica AE Sallese Michele M Makrythanasis Periklis P

International journal of molecular sciences 20251122 23

Marinesco-Sjögren syndrome (MSS) is a rare autosomal recessive neuromuscular disorder marked by ataxia, muscle weakness, cataracts, and often intellectual and skeletal abnormalities. It is commonly caused by loss-of-function variants in the <i>SIL1</i> gene, which impair binding immunoglobulin protein (BiP) function, leading to protein misfolding and activation of the unfolded protein response. In a 2-year-old patient with typical MSS symptoms, we identified a previously unreported c.1024G>A (p. ...[more]

PMID: 41373471

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Project description:Marinesco-Sjogren syndrome (MSS) is a rare multisystem pediatric disorder, caused by loss of function of the endoplasmic reticulum cochaperone SIL1 in about 60% of the patients. SIL1 acts as a nucleotide exchange factor for BiP, which plays a central role in secretory protein folding. SIL1-deficient cells have reduced BiP-assisted protein folding, cannot fulfil their protein needs and experience chronic activation of the unfolded protein response (UPR). Maladaptive UPR may explain the cerebellar and skeletal muscle degeneration re-sponsible for the ataxia and muscle weakness typical of MSS. However, the cause of other, more variable, clinical manifestations, such as mild to severe mental retardation, hypogonadism, short stature and skeletal deformities, are less clear. To gain insights into the pathogenic mechanisms of MSS, we carried out cell bio-logical and proteomic investigations in skin fibroblasts derived from a young patient carrying the SIL1 ... mutation. Despite fibroblasts are not overtly affected in MSS we found morphological and biochemical changes consistent with UPR and metabolic alterations. All the cell machineries involved in RNA splicing and translation were strongly downregulated, while protein degradation via lysosome-based structures was boosted, consistent with an attempt of the cell to reduce the workload of the endoplasmic reticulum and dis-pose misfolded proteins. Cell metabolism was extensively affected as we observed a reduction in lipid syn-thesis, an increase in beta oxidation and an enhancement of the tricarboxylic acid cycle, with upregulation of eight of its enzymes. Finally, the catabolic pathways of various amino acids, including valine, leucine, isoleu-cine, tryptophane, lysine, aspartate and phenylalanine, were enhanced, while the biosynthetic pathways of arginine, serine, glycine and cysteine were reduced. These results indicate profound metabolic alterations in MSS cells in addition to UPR activation and increased protein degradation, which may contribute to make them resistant to SIL1 loss.

Project description:SIL1 acts as a co-chaperone for the major ER-resident chaperone BiP and thus plays a role in many BiP-dependent cellular functions such as protein folding control and unfolded protein response. Whereas increase of BiP upon cellular stress conditions is a well-known phenomenon, elevation of SIL1 under stress conditions was thus far solely studied in yeast and different studies indicated an adverse effect of SIL1 increase. This is seemingly in contrast with the beneficial effect of SIL1 increase in surviving neurons in neurodegenerative disorders such as Amyotrophic Lateral Sclerosis and Alzheimer disease. In the present study, we systematically addressed these controversial findings. Using cell biological, morphological and biochemical methods, we could demonstrate that that SIL1 is increased in various mammalian cells and neuronal tissues upon induction of cellular stress. Investigation of heterozygous SIL1/Sil1 mutant cells and tissues supported this finding. Moreover, SIL1 protein was found to be stabilized during ER stress. Increased SIL1 initiates ER stress in a concentration-dependent manner which is in accordance with the described adverse effect of increased SIL1. However, our results also suggest that protective levels are achieved by the secretion of excessive SIL1 and GRP170 (no longer perturbing ER homeostasis) and that moderately increased SIL1 also ameliorates cellular fitness under stress conditions. Results of our immunoprecipitation studies indicate that under cellular stress conditions SIL1 might act in a BiP-independent manner. Unbiased proteomic studies revealed that elevated SIL1 levels alter the expression of several proteins including crucial players in neurodegeneration, especially in Alzheimer disease. This finding is in accordance with our observation of increased SIL1-immunoreactivity in surviving neurons of Alzheimer disease autopsy cases and supports the assumption that SIL1 plays a protective role in neurodegenerative disorders.

Dataset Information

Structural and functional analysis of the novel pathological variant c.1024G>A in the SIL1 gene causing Marinesco-Sjögren syndrome

Dataset's files

Publications

A Novel <i>SIL1</i> Variant (p.E342K) Associated with Marinesco-Sjögren Syndrome Impairs Protein Stability and Function.

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Dataset Information

Structural and functional analysis of the novel pathological variant c.1024G>A in the SIL1 gene causing Marinesco-Sjögren syndrome

Dataset's files

Publications

A Novel &lt;i&gt;SIL1&lt;/i&gt; Variant (p.E342K) Associated with Marinesco-Sjögren Syndrome Impairs Protein Stability and Function.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

A Novel <i>SIL1</i> Variant (p.E342K) Associated with Marinesco-Sjögren Syndrome Impairs Protein Stability and Function.