A recurrent de novo HSPD1 variant is associated with hypomyelinating leukodystrophy

Abstract

Standardization of the use of next-generation sequencing for the diagnosis of rare neurological disorders has made it possible to detect potential disease-causing genetic variations, including de novo variants. However, the lack of a clear pathogenic relevance of gene variants poses a critical limitation for translating this genetic information into clinical practice, increasing the necessity to perform functional assays. Genetic screening is currently recommended in the guidelines for diagnosis of hypomyelinating leukodystrophies (HLDs). HLDs represent a group of rare heterogeneous disorders that interfere with the myelination of the neurons in the central nervous system. One of the HLD-related genes is HSPD1, encoding the mitochondrial chaperone heat shock protein 60 (HSP60), which functions as folding machinery for the mitochondrial proteins imported into the mitochondrial matrix space. Disease-causing HSPD1 variants have been associated with an autosomal recessive form of fatal hypomyelinating leukodystrophy (HLD4, MitCHAP60 disease; MIM #612233) and an autosomal dominant form of spastic paraplegia, type 13 (SPG13; MIM #605280). In 2018, a de novo HSPD1 variant was reported in a patient with HLD. Here, we present another case carrying the same heterozygous de novo variation in the HSPD1 gene (c.139T > G, p.Leu47Val) associated with an HLD phenotype. Our molecular studies show that the variant HSP60 protein is stably present in the patient's fibroblasts, and functional assays demonstrate that the variant protein lacks in vivo function, thus confirming its disease association. We conclude that de novo variations of the HSPD1 gene should be considered as potentially disease-causing in the diagnosis and pathogenesis of the HLDs.

HSP60 chaperone deficiency disrupts the mitochondrial matrix proteome and dysregulates cholesterol synthesis

“…To evaluate whether disease-associated variations found in patients trigger similar changes in the mitochondrial proteome, we performed proteomics analysis of dermal fibroblasts from two patients carrying disease-associated HSPD1 variants and presenting with hypomyelination phenotype. Patient 1 (P1) is heterozygous for the de novo variation p.Leu47Val with the milder disease phenotype 14 and Patient 2 (P2) is homozygous for the p.Asp29Gly variant causing the severe lethal hypomyelinating leukodystrophy MitCHAP60 disease 12 . Functional assays have shown that both HSP60 variants possess residual chaperone activity 14,15 .…”

“…Patient 1 (P1) is heterozygous for the de novo variation p.Leu47Val with the milder disease phenotype 14 and Patient 2 (P2) is homozygous for the p.Asp29Gly variant causing the severe lethal hypomyelinating leukodystrophy MitCHAP60 disease 12 . Functional assays have shown that both HSP60 variants possess residual chaperone activity 14,15 . In contrast to our D423A-HSP60 cell system, the proteomes of both patient cell lines, each compared to three healthy control individuals, showed mainly upregulation of differentially expressed proteins (Figures 3A and 3B) .…”

“…The effect on mitochondrial matrix protein levels in fibroblast cells from patients carrying disease-associated HSP60 missense variations was very limited in P1 and undetectable in P2. This may be explained by the fact that the dominant-negative and knockout mutations severely shut down HSP60 function in D423A-HSP60 cells and zebrafish larvae, whereas the missense variations in the patients retain residual HSP60 function 14,15 and therefore have a much less pronounced effect on the mitochondrial proteome (Figures 3A and 3B) .…”

“…Because of the broad impact, knocking out HSP60 is lethal in mice and zebrafish 9,10 , and very few genetic HPS60 defects have been detected in human patients. Patients with disease-associated variations in HSP60 present with neurodevelopmental disorders with impaired myelination as a common feature [11][12][13][14][15] . Besides HSPD1 which encodes HSP60, two other genes encoding mitochondrial proteins have been reported to be associated with hypomyelinating leukodystrophies: AIF1, and PYCR2 16,17 .…”

Novel pyrroline-5-carboxylate reductase 2 (PYCR2) mutation in an Iranian patient with hypomyelinating leukodystrophy: findings of molecular and in silico investigations

“…Nevertheless, this procedure is combined with crucial limitations in diagnosis. WES has successfully displayed differential diagnostic efficiency, particularly in rare disease-causing variants, and has a significant potential in identification of de novo mutations [18][19][20].…”