Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways

TLDR

Lysosomes are central to macromolecule degradation and are implicated in disorders, and the CLEAR network with master regulator TFEB orchestrates lysosomal biogenesis and function. The study aimed to identify the essential components of the CLEAR network by defining 471 direct TFEB target genes. The authors employed ChIP‑seq, TFEB‑induced transcription profiling, genome‑wide mapping of TFEB binding sites, and recursive expression meta‑analysis to map these targets. The resulting network regulates lysosomal enzyme expression and activity for protein, glycosaminoglycan, sphingolipid, and glycogen degradation, extends to autophagy, endo/exocytosis, phagocytosis, immune responses, includes non‑lysosomal enzymes, and uncovered nine novel lysosomal proteins, offering therapeutic targets for clearance modulation.

Abstract

In metazoans, lysosomes are the center for the degradation of macromolecules and play a key role in a variety of cellular processes, such as autophagy, exocytosis and membrane repair. Defects of lysosomal pathways are associated with lysosomal storage disorders and with several late onset neurodegenerative diseases. We recently discovered the CLEAR (Coordinated Lysosomal Expression and Regulation) gene network and its master gene transcription factor EB (TFEB), which regulates lysosomal biogenesis and function. Here, we used a combination of genomic approaches, including ChIP-seq (sequencing of chromatin immunoprecipitate) analysis, profiling of TFEB-mediated transcriptional induction, genome-wide mapping of TFEB target sites and recursive expression meta-analysis of TFEB targets, to identify 471 TFEB direct targets that represent essential components of the CLEAR network. This analysis revealed a comprehensive system regulating the expression, import and activity of lysosomal enzymes that control the degradation of proteins, glycosaminoglycans, sphingolipids and glycogen. Interestingly, the CLEAR network appears to be involved in the regulation of additional lysosome-associated processes, including autophagy, exo- and endocytosis, phagocytosis and immune response. Furthermore, non-lysosomal enzymes involved in the degradation of essential proteins such as hemoglobin and chitin are also part of the CLEAR network. Finally, we identified nine novel lysosomal proteins by using the CLEAR network as a tool for prioritizing candidates. This study provides potential therapeutic targets to modulate cellular clearance in a variety of disease conditions.