Project 3


Project 3:
Transcriptional regulation of CLN3 deficiency


Project Summary

Upon a gene-wide expression profiling approach in lymphocytes from CLN3 patients carrying the most common 1-kb deletion in the CLN3 gene and matched controls, we have identified an upregulated dual-specificity phosphatase (1) that negatively regulates the activity of extracellular signal-regulated kinase 2 (ERK2) by dephosphorylation. Among numerous substrates, ERK2 phosphorylate a key regulator of lysosomal biogenesis, autophagy, exocytosis and phagocytosis, transcription factor EB (TFEB) at serine residue 142 (2). In addition to ERK, other kinases have been identified, such as the mTOR kinase complex 1 (mTORC1) that are able to phosphorylate TFEB. TFEB is a member of the microphthalmia-associated transcription factor (MiTF) family that includes MiTF, TFE3, and and TFEC. TFEB functions as homo- or heterodimer with other MiTF members, and is important for transcriptional activation of about 70 lysosome/autophagy-related target genes (among them also NCL genes such as CLN1, CLN2, CLN3, CLN10 and CLN11 (3). When phosphorylated, TFEB remain transcriptionally inactive in the cytosol, and activity and nuclear translocation of TFEB correlate with its phosphorylation status.
This project aims at the identification of lysosomal/autophagy gene targets regulated by the dual-specificity phosphatase and its impact on TFEB using doxycycline-inducible mouse cells. Gene ontology and interactome analysis will be performed followed by further in depth analyses (overexpression, down-regulation, deletion of potential dysregulated candidates in mutant Cln3 cells). These data will be complemented by quantitative proteome analysis of lysosomes in collaboration with SP4.

These data will contribute to a better understanding of molecular pathomechanisms underlying human CLN3 disease.


Potential role of ERK2 phosphatase in TFEB-mediated activation of lysosome/autophagy
target genes (Settembre C et al. Science 332:1429 (2011) modified)



  1. Lebrun A-H, Moll-Khosrawi P, Pohl S, Makrypidi G, Storch S, Kilian D, Streichert T, Otto B, Mole SE, Ullrich K, Cotman S, Kohlschütter A, Braulke T, Schulz A (2011) Analysis of potential biomarkers and modifier genes affecting the clinical course of CLN3 disease.Mol Med 17: 1253-1261
  2. Settembre C, Fraldi A, Medina DL, Ballabio A (2013) Signals from the centre for cellular clearance and energy metabolism. Nat Rev Mol Cell Biol 14: 283-296
  3. Sardiello M, Palmieri M, di Ronza A, Medina DL, Valenza M, Gennarino VA, Di Malta C, Donaudy F, Embrione V, Polishchuk RS, Banfi S, Parenti G, Cattaneo E, Ballabio A (2009) A gene network regulating lysosomal biogenesis and function. Science 325: 473-477