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To elucidate the early pathology, we carried out comparative global transcript profiling of the embryonic, primary cultures of the <jats:italic>Cln3<jats:sup>\u2212\/\u2212<\/jats:sup><\/jats:italic> mouse neurons. Statistical and functional analyses delineated three major cellular pathways or compartments affected: mitochondrial glucose metabolism, cytoskeleton, and synaptosome. Further functional studies showed a slight mitochondrial dysfunction and abnormalities in the microtubule cytoskeleton plus\u2010end components. Synaptic dysfunction was also indicated by the pathway analysis, and by the gross upregulation of the G protein beta 1 subunit, known to regulate synaptic transmission via the voltage\u2010gated calcium channels. Intracellular calcium imaging showed a delay in the recovery from depolarization in the <jats:italic>Cln3<jats:sup>\u2212\/\u2212<\/jats:sup><\/jats:italic> neurons, when the N\u2010type Ca<jats:sup>2+<\/jats:sup> channels had been blocked. The data suggests a link between the mitochondrial dysfunction and cytoskeleton\u2010mediated presynaptic inhibition, thus providing a foundation for further investigation of the disease mechanism underlying JNCL disease. \u00a9 2006 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/jnr.21015","type":"journal-article","created":{"date-parts":[[2006,8,29]],"date-time":"2006-08-29T02:04:37Z","timestamp":1156817077000},"page":"1124-1138","source":"Crossref","is-referenced-by-count":65,"title":["Batten disease (JNCL) is linked to disturbances in mitochondrial, cytoskeletal, and synaptic 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