Rueda, R. | bioRxiv Science

bioRxiv2025

Programmed DNA breaks drive chromatin reconfiguration and facilitate transcriptional potentiation at neuronal early response genes

Neuronal activity causes topoisomerase II{beta} (TOP2B) to form DNA double strand breaks (DSBs) within the promoters of key early response genes (ERGs), such as Fos and Npas4. TOP2B-mediated DSBs facilitate rapid ERG transcription, yet how this occurs remains unclear. Here, using chromosome conformation capture methods (3C and 4C-seq), we report that DSB formation within the promoters of Fos and Npas4 is sufficient to emulate contact profiles observed at these regions following neuronal stimulation, including their elevated interactions with cognate enhancers. Furthermore, despite their purported risk, repeated DSB cycles within ERG promoters progressively potentiated ERG induction in both mouse cortical neurons and HEK293T cells, evoking the effects of transcriptional memory. Potentiated ERG inducibility following recurrent DSBs persisted through intervening cell cycles, occurred even when DNA repair was likely mutagenic, and was associated with a substantial loss of cis chromosome interactions and an increase in trans interactions with ERG promoters. Together, these results reveal how single and recurrent TOP2B-mediated DSBs could affect stimulus-dependent transcription patterns by affecting chromatin dynamics at ERG promoters.

molecular biology↗

bioRxiv2021

Microneedle-mediated intratumoral delivery of anti-CTLA-4 promotes cDC1-dependent eradication of oral squamous cell carcinoma with limited irAEs

Head and neck squamous cell carcinoma (HNSCC) ranks 6th in cancer incidence worldwide and has a five-year survival rate of only 63%. Immunotherapies - principally immune checkpoint inhibitors (ICI), such as anti-PD-1 and anti-CTLA-4 antibodies that restore endogenous antitumor T-cell immunity - offer the greatest promise for HNSCC treatment. Anti-PD-1 has been recently approved for first line treatment of recurrent and metastatic HNSCC; however less than 20% of patients show clinical benefit and durable responses. In addition, the clinical application of ICI has been limited by immune-related adverse events (irAEs) consequent to compromised peripheral immune tolerance. Although irAEs are often reversible, they can become severe, prompting premature therapy termination or becoming life-threatening. To address the irAEs inherent to systemic ICI therapy, we developed a novel, local delivery strategy based upon an array of soluble microneedles (MN). Using our recently reported syngeneic, tobacco-signature murine HNSCC model, we found that both systemic and local-MN anti-CTLA-4 therapy lead to >90% tumor response, which is dependent on CD8 T cells and conventional dendritic cell type 1 (cDC1). However, local-MN delivery limited the distribution of anti-CTLA-4 antibody from areas distal to draining lymphatic basins. Employing Foxp3-GFPDTR transgenic mice to interrogate irAEs in vivo, we found that local-MN delivery of anti-CTLA-4 protects animals from irAEs observed with systemic therapy. Taken together, our findings support the exploration of MN-intratumoral ICI delivery as a viable strategy for HNSCC treatment with reduced irAEs, and the opportunity to target cDC1s as part of multimodal treatment options to boost ICI therapy.

cancer biology↗