Juvenile neuronal ceroid lipofuscinosis (Batten disease) is a neurodegenerative disorder caused by defective function of the lysosomal membrane glycoprotein CLN3. The activity of the lysosomal acid phosphatase (LAP/ACP2) was found to be significantly increased in the cerebellum and brain stem of Cln3-targeted mice during the early stages of postnatal life. Histochemical localization studies revealed an increased LAP/ ACP2 staining intensity in neurons of the cerebral cortex of 48-week-old Cln3-targeted mice as compared with controls. Additionally, the expression of another lysosomal membrane protein LAMP-2 was increased in all brain areas. Knockdown of CLN3 expression in HeLa cells by RNA interference also resulted in increased LAP/ACP2 and LAMP-2 expression. The juvenile form of neuronal ceroid lipofuscinosis (JNCL, Batten disease) is a recessively inherited neurodegenerative disease of childhood which is characterized by initial gliosis and astrocytosis followed by the progressive loss of neurons in the cortex, hippocampus, cerebellum, and the retina . Clinical features include visual loss, mental and motor retardation, epilepsy, and premature death. JNCL belongs to a group of neurodegenerative diseases with defects in ten different genes encoding both soluble and polytopic membrane proteins located in either late endosomes/lysosomes or the endoplasmic reticulum The function of CLN3 is unknown and several processes have been proposed to involve the CLN3 protein such as import of arginine into lysosomes, maturation of autophagic vacuoles, vesicular trafficking, modulation of ceramide synthesis, and apoptosis (Persaud-Sawin et al. 2002, 2004Kim et al. 2003;Luiro et al. 2004;Cao et al. 2006). The role of CLN3 in lysosomal pH homeostasis has been a matter of debate depending on the cell type and model organism being studied reporting either an increase (Pearce Received April 5, 2007; Revised July 27, 2007; Accepted August 6, 2007. Address correspondence and reprint requests to Stephan Storch, Department of Biochemistry, Children's Hospital, University Medical Center Hamburg, D-20246 Hamburg, Germany. E-mail: storch@uke.uni-hamburg.deAbbrevations used: ACP2, human acid phosphatase 2; ACP5, human acid phosphatase 5; ACTB, human b-actin; ActB, mouse b-actin; JNCL, juvenile form of neuronal ceroid lipofuscinosis; LAMP-1, lysosomeassociated membrane protein 1; LAMP-2, lysosome-associated membrane protein 2; LAP, lysosomal acid phosphatase; M6P, mannose 6-phosphate; P week, postnatal week; RT, real-time; siRNA, small interfering RNA; TRAP, tartrate-resistant acid phosphatase.