Analysis of Potential Biomarkers and Modifier Genes Affecting the Clinical Course of CLN3 Disease

Anne-Hélène Lebrun,Sandra Pohl,Georgia Makrypidi,Dirk Kilian,Kurt Ullrich,Alfried Kohlschütter,Susan Cotman,Sara E Mole,Thomas Streichert,Stephan Storch,Parisa Moll-Khosrawi,Benjamin Otto,Thomas Braulke,Angela Schulz

doi:10.2119/molmed.2010.00241

Abstract

Mutations in the CLN3 gene lead to juvenile neuronal ceroid lipofuscinosis, a pediatric neurodegenerative disorder characterized by visual loss, epilepsy and psychomotor deterioration. Although most CLN3 patients carry the same 1-kb deletion in the CLN3 gene, their disease phenotype can be variable. The aims of this study were to (i) study the clinical phenotype in CLN3 patients with identical genotype, (ii) identify genes that are dysregulated in CLN3 disease regardless of the clinical course that could be useful as biomarkers, and (iii) find modifier genes that affect the progression rate of the disease. A total of 25 CLN3 patients homozygous for the 1-kb deletion were classified into groups with rapid, average or slow disease progression using an established clinical scoring system. Genome-wide expression profiling was performed in eight CLN3 patients with different disease progression and matched controls. The study showed high phenotype variability in CLN3 patients. Five genes were dysregulated in all CLN3 patients and present candidate biomarkers of the disease. Of those, dual specificity phosphatase 2 (DUSP2) was also validated in acutely CLN3-depleted cell models and in CbCln3(Δex7/8) cerebellar precursor cells. A total of 13 genes were upregulated in patients with rapid disease progression and downregulated in patients with slow disease progression; one gene showed dysregulation in the opposite way. Among these potential modifier genes, guanine nucleotide exchange factor 1 for small GTPases of the Ras family (RAPGEF1) and transcription factor Spi-B (SPIB) were validated in an acutely CLN3-depleted cell model. These findings indicate that differential perturbations of distinct signaling pathways might alter disease progression and provide insight into the molecular alterations underlying neuronal dysfunction in CLN3 disease and neurodegeneration in general.

Highlights

The neuronal ceroid lipofuscinoses (NCLs) are the most common inherited neurodegenerative disorders mainly affecting children
One of the most frequently occurring NCL forms in Northern European countries is caused by mutations in the CLN3 gene (CLN3 disease, called juvenile NCL or Batten disease)
To investigate whether the clinical variability can be correlated with changes in gene expression, we performed comparative genome-wide microarray analyses in lymphocytes of eight selected CLN3 patients with different rates of disease progression. We identified both genes that are dysregulated in CLN3 disease regardless of the clinical course that might be useful as biomarkers of the disease and genes for which expression correlated with clinical variability, possibly indicating differential expression of modifier genes

Summary

Introduction

The neuronal ceroid lipofuscinoses (NCLs) are the most common inherited neurodegenerative disorders mainly affecting children. Typical symptoms comprise progressive visual loss, psychomotor deterioration and epilepsy. NCLs are incurable lysosomal storage diseases, and lysosomal accumulation of autofluorescent storage material, called ceroid lipofuscin, can be detected in almost all tissues [1]. The most dramatically affected organ is the brain, which undergoes massive neuronal cell atrophy and cell loss [2]. One of the most frequently occurring NCL forms in Northern European countries is caused by mutations in the CLN3 gene (CLN3 disease, called juvenile NCL or Batten disease). CLN3 disease starts at the age of 4–6 years with a progressive retinopathy leading to blindness.

Objectives

Results

Conclusion