Mechanisms underlying subcellular targeting specificities: case studies in pharmacological actions of nitrogen-containing-bisphosphonates and glia-mediated synapse elimination

Abstract

A fundamental phenomenon in biology is the organization of cells into subcellular compartments and structures that contain distinct molecules and perform unique functions. Studying the mechanisms by which biological events occur with subcellular specificity is critical for understanding biological principles and designing precise treatments. This thesis presents investigations into the mechanisms underlying subcellular targeting specificities in two topics: delivery of nitrogen-containing-bisphosphonates (N-BPs) to its pharmacological target, and activity-dependent, glia-mediated synapse elimination during postnatal development. N-BPs are a class of drugs widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies have established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Through a CRISPRi-mediated genome-wide screen, we identified SLC37A3 (solute carrier family 37 member A3) as a gene required for the action of N-BPs in mammalian cells. We discovered that SLC37A3 forms a complex with ATRAID (all-trans-retinoic acid-induced differentiation factor), a previously identified genetic target of N-BPs. SLC37A3 and ATRAID localize to lysosomes and are required for releasing N-BP molecules that have trafficked to lysosomes through fluid-phase endocytosis into the cytosol. During brain development, synapses are initially formed in excess. Redundant synapses are subsequently eliminated in an activity-dependent manner, with weaker synapses being preferentially removed. Recent studies have demonstrated that microglia and astrocytes utilize phagocytic receptors to recognize ‘eat-me’ signals deposited on redundant synapses for synaptic engulfment. However, it is not known how these ‘eat-me’ signals specifically target weaker synapses. Caspase 3, a protease crucial for apoptosis execution, is activated at synapses that are weakened through long-term depression (LTD). In addition, caspase 3 activation during apoptosis triggers the display of various “eat-me” signals recognized by phagocytes for cell debris clearance. We demonstrate that mice deficient in caspase 3 show significant defects in glia-mediated synapse elimination and neural circuit remodeling in the developing visual pathway. We propose that caspase 3 activation at weakened synapses is a key molecular event that links synaptic strength to external signals recognized by glia for synapse removal.