The Repair of Topoisomerase DNA-Protein Crosslinks

Our research is dedicated to elucidating molecular mechanisms that repair topoisomerase DNA-protein crosslinks (TOP-DPCs) and PARP-DNA complexes, whose induction is the primary therapeutic mechanism of topoisomerase inhibitors (TOPi) and PARP inhibitors (PARPi), respectively. We have found that the repair mechanisms are tightly regulated by post-translational modifications such as ubiquitylation-like modifications and polyADP-ribosylation. Ongoing studies involve the investigation of crosstalk between these modifications in the repair of DNA damage induced by topoisomerase inhibitors. (PMID: 33188014, 34408146, 35013556, 36213144, 38055811)

Targeting the repair of TOP-DPCs and PARP-DNA complexes has been proposed as a strategy to improve tumor response to topoisomerase inhibitors and PARP inhibitors. With unbiased high-throughput genetical and chemical screening, we have identified novel DNA repair pathways involved in TOP-DPC repair as well as small molecule inhibitors (SMIs) targeting these pathways. We are interrogating novel combinations of topoisomerase inhibitors and the SMIs in different preclinical cancer models such as lung cancer and colorectal cancer. (PMID: 35830858, 37353483)

We have developed an imaging-based approach enabling real-time monitoring of drug-induced trapping of TOPccs and PARP1 in live cells at the single-molecule level. Capitalizing on this approach, we can measure the fraction of self-fluorescence tag-labeled topoisomerases and PARP single-molecules in real time. Further developing this technique can help us better understand topoisomerase biology and facilitate the development of novel topoisomerase inhibitors. In addition, we are developing methods for labeling antibodies with unique DNA sequences for highly multiplexed detection of topoisomerases and other DNA-binding proteins.  (PMID: 37670571)

Non-specific/non-enzymatic DNA-protein crosslinks (DPCs) are among the most detrimental genomic lesions. They are ubiquitously produced by cellular metabolic by-products and by environmental pollutants such as formaldehyde (FA). Failure to repair these DPCs blocks chromatin-based processes, leading to neurodegeneration and cancer. Yet, the types of proteins crosslinked by aldehydes remain largely unknown. We have profiled the proteome of FA-induced DPCs in human cells. We carried out RNAi screening and found that flap endonuclease 1 (FEN1) and several other nucleases are required for cells to survive FA by repairing FA-induced DPCs. Ongoing studies involve the interrogation of their enzymatic roles in DPC repair. (PMID:39792662)

Topoisomerases play essential roles in DNA replication, transcription, chromosome segregation, and recombination. Insufficient activity in the topoisomerases can generate profound effects on DNA and RNA metabolisms and on the accumulation of non-canonical DNA structures, resulting in cancer, immunodeficiency, and neurological disorders. It is conceivable that cells must have evolved mechanisms to compensate for the genetic inactivation of topoisomerases. We are conducting multiple CRISPR-mediated loss-of-function screens to discover synthetic lethal partners of topoisomerases (TOP1, TOP1MT, TOP2B, TOP3A), which may act as compensatory pathways for topoisomerase-associated cellular processes.

We show that the class I HDAC inhibitor entinostat induces the expression of key immune-related genes and antigen-presenting molecules in small cell lung cancer (SCLC) models and regulates the neuroendocrine status of Rb1/Trp53/MycT58A (RPM) SCLC tumors, enhances T-cell infiltration, and improves the efficacy of anti-PD-1 immunotherapy.   

TOP1i were also reported to upregulate PD-L1 expression and synergize with anti-PD1 immunotherapies. We are exploring pathways involved in the elevation of immunity and antigen presentation, and assessing the combination of immune checkpoint therapy and TOPi. (bioRxiv. 2025.08.06.668958)

Discovery, characterization, and development of first-in-class anti-cancer TOP3A inhibitors

Roles of TOP3B in RNA metabolisms and cellular stress responses and its relevance for human health and diseases

DNA-barcoding antibody customization for multicolor imaging 

Molecular mechanisms of resistance to clinical topoisomerase inhibitors