Our findings show that the transcriptional characterization of braingene expression changes due to the lack of TPP1 during the end stages (at 4 monthsof age) of the disease not only defined the type of neuroinflammation processoccurring but also identified a novel affected pathway (i.e., circadian rhythm),both of which contribute to a better understanding of disease pathophysiology inBatten disease (NCL). Here, TPP1 is linked to glycogen storage disease VI.