Final Report Summary - CLEAR (Modulating cellular clearance to cure human disease)
Using a systems biology approach, we discovered that lysosomal biogenesis and autophagy are transcriptionally regulated by a gene network and by its master gene TFEB, a member of the Helix-Loop-Helix leucine zipper transcription factors. TFEB positively regulates the expression of lysosomal genes, controls the number of lysosomes and promotes all aspects of lysosomal function.
Subsequent studies in our laboratory showed that this regulatory pathway plays a fundamental role in cell homeostasis and mediates the switch between biosynthetic and catabolic pathways during conditions such as starvation. We discovered that TFEB activity responds to environmental cues and is regulated by mTORC1-mediated phosphorylation, which occurs on the lysosomal surface. More recently, we used a TFEB nuclear translocation assay to identify, through siRNA-mediated high content screening, the phosphatase(s) that dephosphorylate TFEB. We discovered that calcineurin, a Ca2+-modulated phosphatase, de-phosphorylates TFEB thus promoting its nuclear translocation. Interestingly, we also found that calcineurin is activated by a lysosomal calcium signalism mechanism mediated by the lysosomal calcium channel mucolipin 1 (MCOLN1). Together these results revealed, for the first time, the presence of lysosome-to-nucleus signaling mechanisms and changed the view of the lysosome from a “suicide bag” to a dynamic organelle that responds to environmental cues. The identification of a global transcriptional regulation of lysosomal function was exploited, by us and by other groups, to boost lysosomal function in mouse models of a variety of disease conditions. Viral-mediated TFEB gene transfer resulted in the clearance of accumulating substrates in cells and tissues from mouse models of several types of LSDs, as well as of Parkinson’s, Alzheimer’s, Huntington’s disease, #1anti-trypsin deficiency, and Spinal Bulbar Muscular Atrophy. These results suggest that transcriptional induction of lysosomal function may represent a novel therapeutic strategy. We are currently testing this possibility using a variety of approaches in collaboration with pharmaceutical companies. Thus, our findings opened a completely new field of investigation (i.e. transcriptional control of lysosomal function) and conceptualized a novel therapeutic strategy (i.e. modulation of cellular clearance) with potential applicability to many diseases.
Subsequent studies in our laboratory showed that this regulatory pathway plays a fundamental role in cell homeostasis and mediates the switch between biosynthetic and catabolic pathways during conditions such as starvation. We discovered that TFEB activity responds to environmental cues and is regulated by mTORC1-mediated phosphorylation, which occurs on the lysosomal surface. More recently, we used a TFEB nuclear translocation assay to identify, through siRNA-mediated high content screening, the phosphatase(s) that dephosphorylate TFEB. We discovered that calcineurin, a Ca2+-modulated phosphatase, de-phosphorylates TFEB thus promoting its nuclear translocation. Interestingly, we also found that calcineurin is activated by a lysosomal calcium signalism mechanism mediated by the lysosomal calcium channel mucolipin 1 (MCOLN1). Together these results revealed, for the first time, the presence of lysosome-to-nucleus signaling mechanisms and changed the view of the lysosome from a “suicide bag” to a dynamic organelle that responds to environmental cues. The identification of a global transcriptional regulation of lysosomal function was exploited, by us and by other groups, to boost lysosomal function in mouse models of a variety of disease conditions. Viral-mediated TFEB gene transfer resulted in the clearance of accumulating substrates in cells and tissues from mouse models of several types of LSDs, as well as of Parkinson’s, Alzheimer’s, Huntington’s disease, #1anti-trypsin deficiency, and Spinal Bulbar Muscular Atrophy. These results suggest that transcriptional induction of lysosomal function may represent a novel therapeutic strategy. We are currently testing this possibility using a variety of approaches in collaboration with pharmaceutical companies. Thus, our findings opened a completely new field of investigation (i.e. transcriptional control of lysosomal function) and conceptualized a novel therapeutic strategy (i.e. modulation of cellular clearance) with potential applicability to many diseases.