Biology subjects

Thibault, C.

Publications and source records attributed to Thibault, C..

4 recordsLinked to original sources

bioRxiv2026

Single-cell trajectories in metastatic urothelial carcinoma reveal tumor-immune reprogramming and macrophage-driven resistance to PD-(L)1 blockade

Immune checkpoint inhibitors (ICI) improved outcomes in metastatic urothelial carcinoma (mUC), but primary and acquired resistance remain poorly understood. We performed single-nuclei RNA sequencing on sequential metastatic biopsies from ICI-treated mUC patients. Tumor cells showed transcriptomic heterogeneity within individual lesions, basal cells being associated with increased immune infiltration and response. Myeloid and lymphoid compartments exhibited features of immune dysfunction in non-responders. Longitudinal analyses revealed convergent adaptive resistance mechanisms, dominated by polarization toward pro-tumoral macrophage states, but also including downregulation of the antigen presentation machinery in tumor cells, increased checkpoint expression with loss of cytotoxicity in T cells. Individual trajectories point to distinct evolutionary routes under ICI pressure. Across pivotal ICI trials, bulk expression of the M2-like macrophage marker HES1 predicted ICI resistance. Our study provides the first single-cell longitudinal atlas of ICI-treated mUC, revealing macrophage reprogramming as a dominant driver of resistance, establishing a framework for individualized immunotherapy strategies.

cancer biology↗

bioRxiv2025

ZIP editors for efficient and versatile CRISPR-Cas9 precise genome editing

Precise genome editing technologies create the potential for genetic studies and innovative gene therapies. Here we present new CRISPR-Cas9 tools, named ZIP CRISPR, loaded with a single-stranded oligodeoxynucleotide (ssODN) template on the Cas ribonucleoprotein complex. The ssODN template is annealed to an extended guide RNA (gRNA) allowing its nuclear delivery at the right place, i.e. the targeted DNA cut, and at the right time. This new template import system is easy-to-design, easy-to-use, inexpensive and versatile. It increases homology-directed repair (HDR) editing efficiency using Cas9 nuclease up to 12-fold with a mean increase of 5-fold as demonstrated at many loci in many cell types. Based on a heteroduplex gRNA-ssODN, it can also be used with the Cas9 nickase, resulting in HDR editing with minimal InDels, and preventing double-strand break (DSB)-mediated genotoxicity. ZIP CRISPR is a non-viral platform adaptable to targeted DSB (higher HDR editing efficiency) or nick (higher safety) to precisely model and correct a wide range of edits. It is suitable for many biological applications and could be considered for HDR-based gene therapies.

bioengineering↗

bioRxiv2021

Nanoscale architecture and coordination of actin cores within the sealing zone of human osteoclasts

Osteoclasts are unique in their capacity to degrade bone tissue. To achieve this process, osteoclasts form a specific structure called the sealing zone, which creates a close contact with bone and confines the release of protons and hydrolases for bone degradation. The sealing zone is composed of actin structures called podosomes nested in a dense actin network. The organization of these actin structures inside the sealing zone at the nano scale is still unknown. Here, we combine cutting-edge microscopy methods to reveal the nanoscale architecture and dynamics of the sealing zone formed by human osteoclasts on bone surface. Random illumination microscopy allowed the identification and live imaging of densely packed actin cores within the sealing zone. A cross-correlation analysis of the fluctuations of actin content at these cores indicates that they are locally synchronized. Further examination shows that the sealing zone is composed of groups of synchronized cores linked by -actinin1 positive filaments, and encircled by adhesion complexes. Thus, we propose that the confinement of bone degradation mediators is achieved through the coordination of islets of actin cores and not by the global coordination of all podosomal subunits forming the sealing zone.

cell biology↗

bioRxiv2021

CROP: A Retromer-PROPPIN complex mediating membrane fission in the endo-lysosomal system

Endo-lysosomal compartments exchange proteins by fusing, fissioning, and through endosomal transport carriers. Thereby, they sort many plasma membrane receptors and transporters and control cellular signaling and metabolism. How the membrane fission events are catalyzed is poorly understood. Here, we identify the novel CROP complex as a factor acting at this step. CROP joins members of two protein families: the peripheral subunits of retromer, a coat forming endosomal transport carriers, and membrane inserting PROPPINs. Integration into CROP potentiates the membrane fission activity of the PROPPIN Atg18 on synthetic liposomes and confers strong preference for binding PI(3,5)P2, a phosphoinositide required for membrane fission activity. Disrupting CROP blocks fragmentation of lysosome-like yeast vacuoles in vivo. CROP-deficient mammalian endosomes accumulate micrometer-long tubules and fail to export cargo, suggesting that carriers attempt to form but cannot separate from these organelles. PROPPINs compete for retromer binding with the SNX proteins, which recruit retromer to the membrane during the formation of endosomal carriers. Transition from retromer-SNX complexes to retromer-PROPPIN complexes might hence switch retromer activities from cargo capture to membrane fission.

cell biology↗