Biology subjects

Mathieu, M.

Publications and source records attributed to Mathieu, M..

8 recordsLinked to original sources

bioRxiv2026

Multi-channel high-density single-molecule localization

Deep learning has enabled single-molecule localization microscopy (SMLM) at high emitter densities, but only for single channel systems. Here we present DECODE-Plex, a deep-learning-based framework to localize dense single molecules with overlapping point spread functions simultaneously in multiple channels. We showcase DECODE-Plex on experimental ultra-high density dual-color and 3D live-cell data. Packaged for ease of use, it will enable many groups to improve imaging speed and quality of multi-channel SMLM.

biophysics↗

bioRxiv2026

Leupaxin inhibits the durotaxis and mechanosensitivity of metastatic breast cancer cells

Efficient cancer cell migration is essential for invasion and metastasis and is driven by cancer cell interaction with their extracellular matrix (ECM). Thus, ECM properties determine the migration phenotype. For example, ECM stiffness can guide cancer cell migration through durotaxis; however, the mechanisms regulating cancer cell durotaxis remain poorly understood. Using in-house stiffness gradient hydrogels, we discovered that MDA-MB-231 breast cancer cell metastatic variants selected for either bone or brain organotropism display impaired durotaxis. Moreover, akin to cells conditioned on soft substrates, these cells have altered mechanoresponses to increasing stiffness, including reduced cell spreading and focal adhesion assembly and signaling. We observed upregulation of the LIM-domain protein leupaxin, a focal adhesion component, in these variants and in soft-conditioned MDA-MB-231 cells compared to parental cells. Leupaxin silencing in brain-tropic metastatic cells restored durotaxis, whereas its overexpression in parental cells impaired durotaxis and mechanosensing, phenocopying the metastatic variants. Mechanistically, leupaxin disrupted paxillin-focal adhesion kinase (FAK) signaling, thereby inhibiting durotaxis. Together, these findings identify leupaxin as a negative regulator of durotaxis in metastatic cells and suggest a mechanism by which tumor cells adapt to mechanical heterogeneity to facilitate metastatic progression.

cell biology↗

bioRxiv2025

Mobilizable adipose stromal cells fuel regenerative adipogenesis in injured muscle

Skeletal muscle regeneration is a highly orchestrated process involving the dynamic interplay of multiple cell types. Among these, fibro-adipogenic progenitors (FAPs), a population of resident mesenchymal stromal cells (MSCs), are essential for creating a supportive microenvironment that promotes satellite cell differentiation and modulates immune responses. Our recent work revealed that adipose stromal cells (ASCs) from subcutaneous adipose tissue (ScAT) infiltrate the injured muscle within the first 24h post-injury, contributing significantly to the regenerative process. Consequently, the FAP population in the regenerating muscle comprises both resident FAPs and infiltrated ASCs. In the present study, using single cell RNA-seq in a mouse model with trackable KikGR+ ASCs and bioinformatics analyses, we identify Limch1+/Prg4+ ASCs as the primary Mobilizable ASCs (Mob-ASCs) that migrate to and infiltrate the injury site. Notably, this migration is detectable as early as 14 hours post-injury. We demonstrate that these cells are pre-activated within the ScAT, primed to initiate both migratory and regenerative programs. Intriguingly, bioinformatic inference of key activated transcription factors suggested that adipogenesis is also activated in these cells. Leveraging supervised machine learning, we tracked the fate of Mob-ASCs within the regenerating muscle post-injury, where they continue to execute these programs. Importantly, these cells lineage is cued towards a fate of adipogenesis. In vivo, we observed transient generation of adipocytes with a peak at 7-9 days post-injury to which infiltrated ASCs contributed. In vitro, conditioned media assays further revealed that adipocytes derived from ASCs--but not those from FAPs--enhance myoblasts fusion. Collectively, our findings establish Limch1+/Prg4+ ASCs as the Mobilizable ASC population and suggest that their transient adipogenic differentiation is beneficial for muscle regeneration.

physiology↗

bioRxiv2025

Macrophages restrict tumor permissiveness to immune infiltration by controlling local collagen topography through a Tcf4-Collagen3 fibrotic axis

During tumorigenesis, the extracellular matrix (ECM), which constitutes the structural scaffold of tissues, is profoundly remodeled. While the impact of such remodeling on tumor growth and invasion has been extensively investigated, much less is known on the consequences of ECM remodeling on tumor infiltration by immune cells. By combining tissue imaging and machine-learning, we here show that the localization of T lymphocytes and neutrophils, which orchestrate antitumor immune responses, can be predicted by defined topographical features of fibrillar collagen networks. We further show that these collagen topographies result from the activation of a fibrotic pathway controlled by the transcription factor Tcf4 upon depletion of tumor-associated macrophages at late tumor stages. This pathway promotes the deposition of collagen 3 by both tumor and stromal cells, resulting in intermingled collagen networks that favor intra-tumoral T cell and neutrophil localization. Importantly, analysis of human colorectal cancer public bulk RNAseq databases showed a strong correlation between Tcf4 and collagen 3, as well as between the expression of these genes and tumor infiltration by T lymphocytes and neutrophils, attesting the clinical relevance of our findings. This study highlights the key structural role of macrophages on the tumor extracellular matrix and identifies collagen network topographies as a major regulator of tumor infiltration by immune cells.

immunology↗

bioRxiv2024

An NAMPT Inhibitor Decreases NAMPT Capture by an Antibody Directed against the 5-Phosphoribosyl-1-Pyrophosphate-Binding Loop: A Rational for an NAMPT Occupancy Assay

Nicotinamide phosphoribosyltransferase (NAMPT) catalyzes the rate-limiting step of nicotinamide adenine dinucleotide (NAD) biosynthesis. NAMPT inhibitors (NAMPTi) have been shown to be NAMPT substrates. The resulting NAMPTi-phosphoribose (RP) adduct binds tightly to NAMPT and inhibits the enzyme. Using new NAMPTi, SAR154782, structural analyses performed in this study unveiled a close proximity of the SAR154782-RP complex to the 5-phosphoribosyl-1-pyrophosphate-binding (PRPP-binding) loop within the NAMPT catalytic site. The PRPP-binding loop of NAMPT is subject to conformational flexibility. Interestingly, the PRPP-binding loop domain is oriented to the outer side of the NAMPT dimer and can potentially serve as an antigen-binding site for antibodies. Here we report for the first time that the NAMPTi-RP adduct bound to NAMPT decreases NAMPT capture by an antibody directed against the c-terminal PRPP-binding loop in NAMPT. This finding was then used to explore cellular NAMPT occupancy. The NAMPTi-RP complex displays a sustained, cellular NAMPT occupancy that correlates with the inhibition of NAMPT activity. Moreover, a good correlation between NAMPT occupancy, NAD decrease, and NAMPTi efficacy was observed in-vivo in a NCI-H82 small cell lung cancer (SCLC) xenograft model. NAMPT-occupancy assay can be used in clinical settings to better define the optimal dose levels and dose regimen for effective NAMPT inhibition.

cancer biology↗

bioRxiv2022

Regulation of cell dynamics by rapid transport of integrins through the biosynthetic pathway

Cells sense and respond to the extracellular matrix (ECM) milieu through integrin proteins. Integrin availability on the plasma membrane, regulated by endosomal receptor uptake and recycling, has been extensively studied and regulates cell dynamics in various normal and pathological contexts1-5. In contrast, the role of integrin transport through the biosynthetic pathway has been considered primarily as a mechanism to replenish the receptor pool and too slow to influence cell dynamics6. Here, we adopted the RUSH (Retention Using Selective Hooks) assay to synchronize integrin anterograde transport from the endoplasmic reticulum (ER), allowing spatial and temporal analysis of newly synthesized receptor traffic. We observe that the delivery of new integrins to the plasma membrane is polarized in response to specific ECM ligands, facilitates integrin recruitment specifically to the membrane-proximal tip of focal adhesions (FA) and contributes to cell protrusion and FA growth. We explain the augmented adhesion growth using a computational molecular clutch model7, where increased integrin availability drives recruitment of additional integrins. Notably, a subset of newly synthesized integrins undergo rapid traffic from the ER to the cell surface to facilitate localized cell spreading, seemingly bypassing the Golgi. This unconventional secretion is dependent on cell adhesion and mediated by Golgi reassembling stacking proteins (GRASPs) association with the PDZ-binding motif in the integrin 5 cytoplasmic tail. This spatially targeted delivery of integrins through the biosynthetic pathway may propel cell dynamics by rapidly altering adhesion receptor availability, providing cells with an additional degree of plasticity to respond to their environment.

cell biology↗

bioRxiv2021

Radiation Exposure of the Base of the Heart Accelerates Coronary Atherosclerosis

Clinical studies have identified cardiac exposure as an independent predictor for cardiovascular mortality in patients treated with radiation therapy (RT) for thoracic malignancies. Although the mechanisms are not completely understood, the available evidence indicate that direct injury to the coronary arteries endothelium is implicated. In these studies we tested the hypothesis that different areas of the heart are more sensitive to the effects of RT on the formation of atherosclerotic plaque in apolipoprotein E deficient (ApoE-/-) mice, a well validated model of atherosclerosis. MethodsApoE-/- mice on a high fat diet (HFD) received 16Gy cardiac irradiation targeted to the whole or partial (apical or basal) region of the heart at 9 weeks or 16 weeks of age. Atherosclerotic lesions and inflammatory changes in the hearts as compared to control unirradiated mice were assessed eight weeks following radiation. ResultsAfter either basal or whole heart RT at 9 weeks of age the number of subendocardial atherosclerotic lesions at the heart base was higher as compared to unirradiated mice. Irradiation of the apex did not increase the number of subendocardial atherosclerotic lesions in any region. After basal RT at 16 weeks of age the number of coronary and subendocardial atherosclerotic lesions was higher as compared to controls. Neither apical or whole heart RT had an impact on the development or acceleration of lesions in the basal region of the hearts of 16 week old mice, thus demonstrating the adverse impact of basal irradiation. Infiltration of inflammatory cells (CD45+ and CD3+) and enhanced expression of endothelial adhesion molecules (CD31), were differentially and locally regulated based upon the site of irradiation. In support of a role of eicosanoid mediators for base or whole heart atherogenic irradiation effects, apex irradiation eicosanoid mediators are not clearly atherogenic, in contrast to eicosanoid mediators detected in serum after base heart irradiation. These results indicate that the base of the heart is significantly more prone to the development of atherosclerotic lesions in the coronary arteries post-RT. ConclusionOur results indicate that the base of the heart is more susuceptible to development of RT-induced atherosclerotic lesions and therefore avoidance from RT direct exposure to this area may reduce the risk for atherosclerotic disease in patients undergoing RT.

cancer biology↗

bioRxiv2020

Specificities of exosome versus small ectosome secretion revealed by live intracellulartracking and synchronized extracellular vesicle release of CD9 and CD63

Despite their important and multiple roles in intercellular communications, the different populations of extracellular vesicles (EVs) and their secretion mechanisms are not fully characterized yet. In particular, how and to what extent EVs form either as intraluminal vesicles of endocytic compartments (exosomes), or at the plasma membrane (ectosomes) remains unclear. We followed in HeLa cells the intracellular trafficking of the EV markers CD9 and CD63 from the endoplasmic reticulum to their residency compartment and identified transient co-localization both at the plasma membrane (PM) and in endosomes, before they finally segregate. CD9 was more abundantly released in EVs than CD63. However, when forcing expression of CD63 at the PM, by mutating its lysosome-addressing motive, its secretion in EVs was increased. Thus, in HeLa cells, small ectosomes are more prominently released than exosomes. By comparative proteomic analysis, we identified a few surface proteins likely specific of either exosomes (e.g. LAMP1) or ectosomes (e.g. BSG, SLC3A2), based on their known intracellular location in lysosomes or the PM, and on the different effects on their release of Bafilomycin A1, a drug that neutralizes endosomal pH. Our work sets the path for molecular and functional discrimination of exosomes and small ectosomes in any cell type.

cell biology↗