Biology subjects

Pham, F.

Publications and source records attributed to Pham, F..

3 recordsLinked to original sources

bioRxiv2026

Non-covalent reversibly photoconvertible fluorescent tags for wash-free protein labeling

Reversibly photoswitchable fluorophores are widely used in advanced bioimaging but their design remains demanding. Here, we introduce a new series spanning the whole visible range, which results from combining a large set of fluorogens with the FAST protein scaffold. We first demonstrate that these well-established labeling fluorescent protein tags turn into negative reversible photoswitchers upon decreasing the fluorogen concentration and increasing light intensity. We then show that using not anymore one but two fluorogens adds new responses to illumination. Thus, we obtain positive reversible photoswitchers, that increase their brightness under illumination. We also generate a palette of non-covalent reversibly photoconvertible fluorescent proteins changing their fluorescence color upon illumination, a reversible behavior that still remains absent in regular fluorescent proteins. This light-induced color change opens the possibility to discriminate six spectrally similar FAST variants in live cells upon demonstrating the superiority of using multiple spectral channels for exploiting the time dependence of the fluorescence response to illumination.

biophysics↗

bioRxiv2025

Spatial tumour-immune ecosystems shape the efficacy of anti-PD1 immunotherapy in primary cutaneous melanoma

Intra-tumoral heterogeneity in melanoma arises from dynamic cancer cell plasticity and underlies various mechanisms of immune escape. Here, we combined high-plex immunofluorescence imaging with spatially resolved transcriptomics to map the architecture of melanoma cell states and their interactions with the immune microenvironment in primary cutaneous tumours prior to adjuvant anti-PD1 immune checkpoint inhibitor (ICI) treatment. Computational analyses showed that melanoma cells organise into spatially restricted patches, with a preferential organisation of undifferentiated cells associated with poor ICI efficacy. Neighbouring immune cell composition varied according to cancer cell states, with a crucial involvement of specific subsets of tumour-associated macrophages, driven by signalling pathways involving tumour-derived and microenvironmental cues such as IFN-{gamma} and hypoxia. Integrated spatial analyses further revealed tumour-immune ecosystems that stratify patient outcomes, delineating configurations either associated with ICI efficacy or metastatic relapse. These results uncover the spatial landscape of tumour ecosystems and identify signalling pathways as potential targets for improving the efficacy of ICI in melanoma. HighlightsO_LIMelanoma cell states spatial organization is associated with aPD1 therapy efficacy C_LIO_LISpatial organization of TAM subsets is a crucial determinant of ICI outcome C_LIO_LIMelanoma cells in different states co-localise with functionally distinct TAM subsets C_LIO_LIIdentification of cell-cell communication pathways that underlie tumour-TAM crosstalk C_LIO_LIA balance between tumour-immune ecosystems is associated with aPD1 therapy efficacy C_LI

cancer biology↗

bioRxiv2025

The epigenetic regulator TRIM24 controls melanoma cell dedifferentiation and resistance to treatment in melanoma

Cancer cell plasticity plays a key role in tumor progression and treatment resistance in melanoma. While the transcriptional programs enabling adaptative switching between melanocytic and mesenchymal phenotypes are well characterized, unravelling druggable epigenetic regulators that sustain melanoma cell adaptation and resistance remains crucial. Herein, we identified TRIM24, a bromodomain protein frequently upregulated during melanoma metastatic progression, as a crucial regulator of melanoma cell plasticity towards invasive/resistant states. shRNA-mediated knock-down of TRIM24 or degradation using a TRIM24-specific PROTAC decrease the migratory capacities and increase the sensitivity to BRAF inhibitors of melanoma cells. Integration of transcriptomic (RNA-seq) and epigenomic (ATAC-seq, CUT&Tag) analyses reveals that TRIM24 reprograms the epigenome of melanoma cells, promoting mesenchymal and repressing melanocytic transcriptional programs. We further define a TRIM24-specific transcriptional signature, that is consistently enriched in treatment-resistant mesenchymal subpopulations in melanoma single-cell RNA-seq datasets. Accordingly, analysis of TRIM24 protein expression in melanoma patients highlights that high TRIM24 expression correlates with relapse to adjuvant immunotherapy. Finally, TRIM24 knock-down in immunocompetent mouse models synergises with immune checkpoint inhibitors. Overall, our findings spotlight TRIM24 as a major epigenetic regulator driving melanoma cell dedifferentiation and resistance to therapy, representing a promising druggable target to reverse phenotype switching and resensitize to treatment.

cancer biology↗