Biology subjects

Lefort, S.

Publications and source records attributed to Lefort, S..

4 recordsLinked to original sources

bioRxiv2024

Modeling relaxation experiments with a mechanistic model of gene expression

BackgroundIn the present work, we aimed at modeling a relaxation experiment which consists in selecting a subfraction of a cell population and observing the speed at which the entire initial distribution for a given marker is reconstituted. MethodsFor this we first proposed a modification of a previously published mechanistic two-state model of gene expression to which we added a state-dependent proliferation term. This results in a system of two partial differential equations. Under the assumption of a linear proliferation rate, we could derive the asymptotic profile of the solutions of this model. ResultsIn order to confront our model with experimental data, we generated a relaxation experiment of the CD34 antigen on the surface of TF1-BA cells, starting either from the highest or the lowest CD34 expression levels. We observed in both cases that after approximately 25 days the distribution of CD34 returns to its initial stationary state. Numerical simulations, based on parameter values estimated from the dataset, have shown that the model solutions closely align with the experimental data from the relaxation experiments. ConclusionAltogether our results strongly support the notion that cells should be seen and modeled as probabilistic dynamical systems.

systems biology↗

bioRxiv2021

{-}CardiOvascular examination in awake Orangutans (Pongo pygmaeus pygmaeus): Low-stress Echocardiography including Speckle Tracking imaging (the COOLEST method)

IntroductionCardiovascular diseases have been identified as a major cause of mortality and morbidity in Borneo orangutans (Pongo pygmaeus pygmaeus). Transthoracic echocardiography is usually performed under anesthesia in great apes, which may be stressful and risky in cardiac animals. The aim of the present pilot study was hence to develop a quick and non-stressful echocardiographic method (i.e., the COOLEST method) in awake Borneo orangutans (CardiOvascular examination in awake Orangutans: Low-stress Echocardiography including Speckle Tracking imaging) and assess the variability of corresponding variables. Materials and MethodsFour adult Borneo orangutans trained to present their chest to the trainers were involved. A total of 96 TTE examinations were performed on 4 different days by a trained observer examining each orangutans 6 times per day. Each examination included four two-dimensional views, with offline assessment of 28 variables (i.e., two-dimensional (n=12), M-mode and anatomic M-mode (n=6), Doppler (n=7), and speckle tracking imaging (n=3)), representing a total of 2,688 measurements. A general linear model was used to determine the within-day and between-day coefficients of variation. ResultsMean{+/-}SD (minimum-maximum) images acquisition duration was 3.8{+/-}1.6 minutes (1.3-6.3). All within-day and between-day coefficients of variation but one (n=55/56, 98%) were <15%, and most (51/56, 91%) were <10% including those of speckle tracking systolic strain variables (2.7% to 5.4%). DiscussionHeart morphology as well as global and regional myocardial function can be assessed in awake orangutans with good to excellent repeatability and reproducibility. ConclusionsThis non-stressful method may be used for longitudinal cardiac follow-up in awake orangutans.

zoology↗

bioRxiv2020

Development of a soft cell confiner to decipher the impact of mechanical stimuli on cells

Emerging evidence suggests the importance of mechanical stimuli in normal and pathological situations for the control of many critical cellular functions. While the effect of matrix stiffness has been and is still extensively studied, few studies have focused on the role of mechanical stresses. The main limitation of such analyses is the lack of standard in vitro assays enabling extended mechanical stimulation compatible with dynamic biological and biophysical cell characterization. We have developed an agarose-based microsystem, the soft cell confiner, which enables the precise control of confinement for single or mixed cell populations. The rigidity of the confiner matches physiological conditions and enables passive medium renewal. It is compatible with time-lapse microscopy, in situ immunostaining, and standard molecular analyses, and can be used with both adherent and non-adherent cell lines. Cell proliferation of various cell lines (hematopoietic cells, MCF10A epithelial breast cells and HS27A stromal cells) was followed for several days up to confluence using video-microscopy and further documented by Western blot and immunostaining. Interestingly, even though the nuclear projected area was much larger upon confinement, with many highly deformed nuclei (non-circular shape), cell viability, assessed by live and dead cell staining, was unaffected for up to 8 days in the confiner. However, there was a decrease in cell proliferation upon confinement for all tested cell lines. The soft cell confiner is thus a valuable tool to decipher the effect of long-term confinement and deformation on the biology of cell populations. This tool will be instrumental in deciphering the impact of nuclear and cytoskeletal mechanosensitivity in normal and pathological conditions involving highly confined situations, such as those reported upon aging with fibrosis or during cancer. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY A unique tool to analyze the role of long-term effect of mechanical confinement in normal and pathological conditions

biophysics↗

bioRxiv2018

YB-1 Is Critical For The Genesis And Progression Of KRAS Mutated Human Breast Cancer

Breast cancer heterogeneity has made it challenging to elucidate shared mechanisms that underpin properties that are critical to their growth in vivo. Here, we interrogate the role of YB-1 protein in the in vivo tumorigenic activity of de novo well as cell line models of human breast cancer. Short-hairpin RNA-mediated knockdown of YB-1 in MDA-MB-231 cells blocked both their local tumour-forming and lung-colonizing activity in transplanted immunodeficient mice. YB-1 knockdown also revealed its important role at early stages of human mammary cell transformation in the generation of invasive ductal carcinoma and ductal carcinoma in situ produced in mice transplanted with freshly isolated human mammary cells transduced, respectively, with KRASG12D, or myristoylated-AKT1. Conversely, upregulated expression of YB-1 in the poorly tumorigenic T47D cells enhanced this activity. Mechanistically, reducing YB-1 levels in MDA-MB-231 cells impaired their induction of HIF1, and G3BP1, known YB-1 translational targets and key elements of a stress-adaptive program.

cancer biology↗