Biology subjects

Schulze, N.

Publications and source records attributed to Schulze, N..

4 recordsLinked to original sources

bioRxiv2025

Targeted degradation of USP7 in solid cancer cells reveals disparate effects of deubiquitinase inhibition vs. acute protein depletion

Proteolysis-targeting chimeras (PROTACs) co-op the ubiquitin system for targeted protein degradation, creating opportunities to interrogate cellular functions of proteins through "chemical knockdown". However, matched pairs of protein degraders and inhibitors, that possess high specificity and chemical complementarity, for individual components of the ubiquitin system have remained scarce. This includes reagents to modulate activity and abundance of deubiquitinases (DUBs), which critically regulate ubiquitin-mediated signaling. Here, using an integrated chemical biology approach, we explored the cellular function of the DUB USP7 as a case study comparing inhibition and degradation of this DUB in melanoma and pancreatic cancer cells. Through the synthesis of a degrader library, we identified potent USP7 PROTACs for each cancer type, established BRET-based ternary complex formation and quantified degradation efficiency. USP7 degraders and their cognate inhibitor were subsequently employed to characterize treatment-induced phenotypic alterations. Proteomic and cellular analyses revealed that highly specific degradation of USP7 modulated both shared and distinct protein sets across cancer cell types, without impacting cell growth. Notably, cellular responses to USP7 degradation differed markedly from those to USP7 inhibition. Moreover, our data uncovered broad proteomic and metabolic changes induced by prolonged USP7 inhibitor treatment. Collectively, our work provides a chemical toolbox of comprehensively characterized reagents to distinguish on-target phenotypes which will aid the understanding of the role of USP7 in malignant diseases. More broadly, our data emphasize the importance of increased specificity via PROTAC-mediated degradation and the potential of this modality to distinguish catalytic from non-catalytic as well as cell-line specific functions of DUBs.

biochemistry↗

bioRxiv2025

ATXN3 regulates lysosome regeneration after damage by targeting K48-K63-branched ubiquitin chains

The cellular response to lysosomal damage involves fine-tuned mechanisms of membrane repair, lysosome regeneration and lysophagy, but how these different processes are coordinated is not fully understood. Here we show in human cells that the deubiquitinating enzyme ATXN3 helps restore integrity of the lysosomal system after damage by targeting K48-K63-linked branched ubiquitin chains on regenerating lysosomes. We find that ATXN3 translocates to lysosomes after different types of damage and there colocalizes with its partner, VCP/p97. ATXN3 recruitment occurs late after the initial repair of a subset of lysosomes and after phagophore formation on terminally damaged lysosomes. Of note, inactivation of ATXN3 by induced degradation, depletion or knock-out impairs clearance of damaged lysosomes and full restoration of lysosomal capacity. Mechanistically, ATXN3, along with VCP/p97, turns over K48-K63-branched ubiquitin conjugates on LAMP1-positive, phosphatidylinositol-(4,5)-bisphosphate-decorated compartments that are not yet fully re-acidified indicating involvement in lysosome regeneration. Our findings identify a key role of ATXN3 in restoring lysosomal function after lysosomal membrane damage and uncover K48-K63-branched ubiquitin chain-regulated regeneration as a critical element of the lysosomal damage stress response.

cell biology↗

bioRxiv2025

Optogenetic stimulation of Lbc GEF-mediated Rho activity dynamics promotes cell invasion

Cancer cell invasion relies on dynamic cell shape changes, which originate from protrusive and contractile intracellular forces. Previous studies revealed that contractile forces are controlled by positive-feedback amplification of the contraction regulator Rho by Lbc GEFs. These GEFs were previously linked to tumor progression, however, the underlying mechanisms are poorly understood. Here, we generated a mouse melanoma model, in which cytosolic levels of the Lbc GEF GEF-H1 are controlled by light. Using this model, we found that increased GEF-H1 levels strongly stimulate cell contraction dynamics. Interestingly, increased contraction dynamics rapidly induced expansion of tumor spheroids via a focal adhesion kinase-dependent mechanism. Furthermore, long-term stimulation led to the escape of individual cells from spheroids. These findings reveal new insights into the oncogenic roles of Lbc GEFs, and how they might promote tumor cell invasion. We propose a mechanism, in which increased cell contraction dynamics results in asymmetric pulling forces at the tumor border, promoting the detachment and escape of individual cells.

cell biology↗

bioRxiv2024

A non-autonomous protein quality control mechanism targeting tau aggregate propagation

Tauopathies such as Alzheimers disease, frontotemporal dementia with Parkinsonism, and other neurodegenerative disorders are characterized by the spread of tau pathology from an initial brain region to neuroanatomically connected areas. At the molecular level, spreading involves aggregation of tau in a donor cell, externalization of transmissible fragments of amyloid fibrils, internalization by an acceptor cell, followed by seeded aggregation of endogenous tau. However, the protein quality control mechanisms that counteract tau aggregation, and in particular its spreading process, are not well understood. In this context, a co-migrating factor performing location-independent interference of fibril formation and transmission would be an appropriate conceptual solution. Here, we show that the cell-to-cell transfer of the widely conserved serine protease HTRA1 impedes tau pathology by targeting multiple steps within the spreading process. Our results suggest a defense mechanism against the intercellular spread of pathogenic protein conformations.

biochemistry↗