Molecular Medicine

, Volume 17, Issue 11–12, pp 1253–1261 | Cite as

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

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


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 CbCln3Δex7/8 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.



We thank the affected and control families for participating in this study and Johannes Brand for technical assistance. This work was supported by the Deutsche Forschungsgemeinschaft (grant SCHU1597/2–1) and the parent organizations Nächstenliebe e.V. and NCL-Gruppe Deutschland e.V.

Supplementary material

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  1. 1.
    Jalanko A, Braulke T. (2009) Neuronal ceroid lipofuscinoses. Biochim. Biophys. Acta. 1793:697–709.CrossRefGoogle Scholar
  2. 2.
    Haltia M. (2003) The neuronal ceroid-lipofuscinoses. J. Neuropathol. Exp. Neurol. 62:1–13.CrossRefGoogle Scholar
  3. 3.
    Williams RE, et al. (2006) Diagnosis of the neuronal ceroid lipofuscinoses: an update. Biochim. Biophys. Acta. 1762:865–72.CrossRefGoogle Scholar
  4. 4.
    International Batten Disease Consortium. (1995) Isolation of a novel gene underlying Batten disease, CLN3. Cell. 82:949–57.CrossRefGoogle Scholar
  5. 5.
    Munroe PB, et al. (1997) Spectrum of mutations in the Batten disease gene, CLN3. Am. J. Hum. Genet. 61:310–6.CrossRefGoogle Scholar
  6. 6.
    Kyttälä A, Lahtinen U, Braulke T, Hofmann SL. (2006) Functional biology of the neuronal ceroid lipofuscinoses (NCL) proteins. Biochim. Biophys. Acta. 1762:920–33.CrossRefGoogle Scholar
  7. 7.
    Kohlschütter A, Laabs R, Albani M. (1988) Juvenile neuronal ceroid lipofuscinosis (JNCL): quantitative description of its clinical variability. Acta. Paediatr. Scand. 77:867–72.CrossRefGoogle Scholar
  8. 8.
    Fossale E, et al. (2004) Membrane trafficking and mitochondrial abnormalities precede subunit c deposition in a cerebellar cell model of juvenile neuronal ceroid lipofuscinosis. BMC Neurosci. 5:57.CrossRefGoogle Scholar
  9. 9.
    Pohl S, et al. (2007) Increased expression of lysosomal acid phosphatase in CLN3-defective cells and mouse brain tissue. J. Neurochem. 103:2177–88.CrossRefGoogle Scholar
  10. 10.
    Ashburner M, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25:25–9.CrossRefGoogle Scholar
  11. 11.
    Lou HC, Kristensen K. (1973) A clinical and psychological investigation into juvenile amaurotic idiocy in Denmark. Dev. Med. Child Neurol. 15:313–23.CrossRefGoogle Scholar
  12. 12.
    Sorensen JB, Parnas J. (1979) A clinical study of 44 patients with juvenile amaurotic family idiocy. Acta. Psychiatr. Scand. 59:449–61.CrossRefGoogle Scholar
  13. 13.
    Adams HR, et al. (2010) Genotype does not predict severity of behavioural phenotype in juvenile neuronal ceroid lipofuscinosis (Batten disease). Dev. Med. Child. Neurol. 52:637–53.CrossRefGoogle Scholar
  14. 14.
    Hofman IL, van der Wal AC, Dingemans KP, Becker AE. (2001) Cardiac pathology in neuronal ceroid lipofuscinoses: a clinicopathologic correlation in three patients. Eur. J. Paediatr. Neurol. 5:213–7.CrossRefGoogle Scholar
  15. 15.
    Tomiyasu H, et al. (2000) An autopsy case of juvenile neuronal ceroid-lipofuscinosis with dilated cardiomyopathy. Rinsho. Shinkeigaku. 4:350–7.Google Scholar
  16. 16.
    Kohlschütter A, Schulz A. (2009) Towards understanding the neuronal ceroid lipofuscinoses. Brain Dev. 31:499–502.CrossRefGoogle Scholar
  17. 17.
    Anderson G, Smith VV, Malone M, Sebire NJ. (2005) Blood film examination for vacuolated lymphocytes in the diagnosis of metabolic disorders; retrospective experience of more than 2,500 cases from a single centre. J. Clin. Pathol. 58:1305–10.CrossRefGoogle Scholar
  18. 18.
    Mole SE, Williams RE, Goebel HH. (2005) Correlations between genotype, ultrastructural morphology and clinical phenotype in the neuronal ceroid lipofuscinoses. Neurogenetics. 6:107–26.CrossRefGoogle Scholar
  19. 19.
    Patterson KI, Brummer T, O±Brien PM, Daly RJ. (2009) Dual-specificity phosphatases: critical regulators with diverse cellular targets. Biochem. J. 418:475–89.CrossRefGoogle Scholar
  20. 20.
    Yin Y, Liu YX, Jin YJ, Hall EJ, Barrett JC. (2003) PAC1 phosphatase is a transcription target of p53 in signalling apoptosis and growth suppression. Nature. 422:527–31.CrossRefGoogle Scholar
  21. 21.
    Boschert U, Muda M, Camps M, Dickinson R, Arkinstall S. (1997) Induction of the dual specificity phosphatase PAC1 in rat brain following seizure activity. Neuroreport. 8:3077–80.CrossRefGoogle Scholar
  22. 22.
    Givant-Horwitz V, et al. (2004). The PAC-1 dual specificity phosphatase predicts poor outcome in serous ovarian carcinoma. Gynecol. Oncol. 93:517–32.CrossRefGoogle Scholar
  23. 23.
    Luiro K, et al. (2006) Batten disease (JNCL) is linked to disturbances in mitochondrial, cytoskeletal, and synaptic compartments. J. Neurosci. Res. 84:1124–38.CrossRefGoogle Scholar
  24. 24.
    Knudsen BS, Feller SM, Hanafusa H. (1994) Four proline-rich sequences of the guanine-nucleotide exchange factor C3G bind with unique specificity to the first Src homology 3 domain of Crk. J Biol. Chem. 269:32781–7.PubMedGoogle Scholar
  25. 25.
    Tanaka S, et al. (1994) C3G, a guanine nucleotide-releasing protein expressed ubiquitously, binds to the Src homology 3 domains of CRK and GRB2/ASH proteins. Proc. Natl. Acad. Sci. U. S. A. 91:3443–7.CrossRefGoogle Scholar
  26. 26.
    D±Arcangelo G, et al. (1995) A protein related to extracellular matrix proteins deleted in the mouse mutant reeler. Nature. 374:719–23.CrossRefGoogle Scholar
  27. 27.
    Voss AK, et al. (2008) C3G regulates cortical neuron migration, preplate splitting and radial glial cell attachment. Development. 135:2139–49.CrossRefGoogle Scholar
  28. 28.
    Schotte R, Nagasawa M, Weijer K, Spits H, Blom B. (2004) The ETS transcription factor Spi-B is required for human plasmacytoid dendritic cell development. J. Exp. Med. 200:1503–9.CrossRefGoogle Scholar
  29. 29.
    Anderson MK. (2006) At the crossroads: diverse roles of early thymocyte transcriptional regulators. Immunol. Rev. 209:191–211.CrossRefGoogle Scholar
  30. 30.
    Aula P, Rapola J, Andersson LC. (1975) Distribution of cytoplasmic vacuoles in blood T and B lymphocytes in two lysosomal disorders. Virchows Arch. B Cell Pathol. 18:263–71.PubMedGoogle Scholar
  31. 31.
    Bruck W, Goebel HH, Dienes P. (1991) B and T lymphocytes are affected in lysosomal disorders: an immunoelectron microscopic study. Neuropathol. Appl. Neurobiol. 17:219–22.CrossRefGoogle Scholar
  32. 32.
    von Schantz C, et al. (2008) Brain gene expression profiles of Cln1 and Cln5 deficient mice unravels common molecular pathways underlying neuronal degeneration in NCL diseases. BMC Genomics. 9:146.CrossRefGoogle Scholar
  33. 33.
    Elshatory Y, et al. (2003) Early changes in gene expression in two models of Batten disease. FEBS Lett. 538:207–12.CrossRefGoogle Scholar
  34. 34.
    Chattopadhyay S, et al. (2004) Altered gene expression in the eye of a mouse model for batten disease. Invest. Ophthalmol. Vis. Sci. 45:2893–905.CrossRefGoogle Scholar
  35. 35.
    Brooks AI, Chattopadhyay S, Mitchison HM, Nussbaum RL, Pearce DA. (2003) Functional categorization of gene expression changes in the cerebellum of a Cln3-knockout mouse model for Batten disease. Mol. Genet. Metab. 78:17–30.CrossRefGoogle Scholar

Copyright information

© The Feinstein Institute for Medical Research 2011

Authors and Affiliations

  • Anne-Hélène Lebrun
    • 1
  • Parisa Moll-Khosrawi
    • 1
  • Sandra Pohl
    • 1
  • Georgia Makrypidi
    • 1
  • Stephan Storch
    • 1
  • Dirk Kilian
    • 1
  • Thomas Streichert
    • 2
  • Benjamin Otto
    • 2
  • Sara E. Mole
    • 3
  • Kurt Ullrich
    • 1
  • Susan Cotman
    • 4
  • Alfried Kohlschütter
    • 1
  • Thomas Braulke
    • 1
  • Angela Schulz
    • 1
  1. 1.Children’s HospitalUniversity Medical Center Hamburg-Eppendorf Martinistrasse 52HamburgGermany
  2. 2.Array Service CenterUniversity Medical Center Hamburg-EppendorfHamburgGermany
  3. 3.Medical Research Council Laboratory for Molecular Cell Biology, Molecular Medicine Unit, UCL Institute of Child Health and Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
  4. 4.Center for Human Genetic ResearchMassachusetts General HospitalBostonUSA

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