Biology subjects

Perrin, J.

Publications and source records attributed to Perrin, J..

3 recordsLinked to original sources

bioRxiv2026

LiFT: Live foci tracking for quantitative analysis of DNA damage dynamics

Quantitative analysis of radiation induced DNA double strand breaks (DSBs) and their repair is essential for understanding and eventually contributing to improving radiation-based cancer therapies. Using live-cell microscopy, the formation and resolution of DSBs over time can be followed in individual cells through tracking of foci formed by accumulation of DSB repair proteins. However, manual analysis of such time-lapse datasets is a tedious time-consuming task that is prone to operator bias, affecting the reproducibility. Here, we present LiFT, an automated image analysis pipeline, specifically designed for robust quantification of DSB kinetics in live-cell imaging experiments. To quantify DSB kinetics, our pipeline first segments and tracks cell nuclei without requiring a nuclear stain. After correcting for inter-frame motion through image registration, automatic detection and tracking of foci within these nuclei enables direct quantification of the dynamics of individual repair events. Multiple algorithmic options were implemented for each step of the pipeline, ensuring more general applicability to potentially different imaging setups and applications. We evaluated the pipeline using PLC/PRF/5 cells and demonstrated its generalizability on U2OS-SSTR2 cells. Our results show that LiFT enables reproducible and scalable quantification of DSB dynamics, providing a broadly applicable framework to analyse live-cell imaging data in cancer research. To improve the adoption of LiFT, we made it available as an open-source Python package and provided a graphical user interface to select different methods and adjust method related parameters.

bioinformatics↗

bioRxiv2024

A cellular assay to determine the fusion capacity of MFN2 variants linked to Charcot-Marie-Tooth type 2A

Charcot-Marie-Tooth Disease (CMT) is an inherited peripheral neuropathy with two main forms: demyelinating CMT1 and axonal CMT2. The most frequent subtype of CMT2 (CMT2A) is linked to mutations of MFN2, encoding a membrane-anchored GTP-binding protein essential for mitochondrial outer membrane fusion. The use of Next-Generation Sequencing for genetic analysis has led to the identification of increasing numbers of MFN2 variants, but a majority of them remain variants of unknown significance, depriving patients of a clear diagnosis. In this work, we establish a cellular assay allowing to assess the impact of MFN2 variants linked to CMT2A on the fusion capacity of MFN2. The analysis of 12 MFN2 variants revealed that five abolish fusion, one induces an important reduction and six retain a fusion capacity similar to that of wild-type MFN2. Their analysis with computational variant effect predictors demonstrated a remarkable correlation of our results with predictions based on protein sequence analysis. This work develops novel tools to determine the functional impact of known and novel MFN2 variants and identifies computational tools allowing to predict their possible consequences and pathogenicity.

cell biology↗

bioRxiv2018

Proteome thermal stability reflects organ physiology and identifies drug-target engagement in vivo

Studying biological processes at a molecular level and monitoring drug-target interactions is established for simple cell systems but challenging in vivo. We introduce and apply a methodology for proteome-wide thermal stability measurements to characterize organ physiology and activity of many fundamental biological processes across tissues, such as energy metabolism and protein homeostasis. This method, termed tissue thermal proteome profiling (tissue-TPP), also enabled target and off-target identification and occupancy measurements in tissues derived from animals dosed with the non-covalent histone deacetylase inhibitor, panobinostat. Finally, we devised blood-CETSA, a thermal stability-based method to monitor target engagement in whole blood. Our study generates the first proteome-wide map of protein thermal stability in tissue and provides tools that will be of great impact for translational research.

cell biology↗