Biology subjects

Thevenin, D.

Publications and source records attributed to Thevenin, D..

10 recordsLinked to original sources

bioRxiv2026

Systems modeling identifies phenotype-determining signaling pathways controlled by phosphatase PTPRJ in diverse receptor tyrosine kinase activation settings

Protein tyrosine phosphatase receptor J (PTPRJ) restrains cell proliferation and migration by dephosphorylating receptor tyrosine kinases (RTKs) including the epidermal growth factor receptor (EGFR). PTPRJ is a purported tumor suppressor, and alterations to its expression and/or function are associated with colorectal, breast, lung, and other cancers. While there is interest in controlling PTPRJ-regulated phenotypes, efforts are limited by the complexity of PTPRJ-mediated signaling. PTPRJ dephosphorylates multiple RTKs, and the degree to which PTPRJ control of signaling and phenotypes depends on local cellular RTK activation profiles is unknown. To probe the context dependence of PTPRJ signaling regulation, we collected signaling measurements across 16 pathway nodes at two time points in a panel of HSC3 carcinoma cells engineered with different PTPRJ expression profiles. Cells were treated with three different RTK ligands, and paired phenotype measurements (viability, wound healing, xCELLigence cell index) were made. Partial least squares regression models were developed to predict relationships between PTPRJ-regulated signaling pathways and cell phenotypes. The model effectively separated contributions to variance arising from the PTPRJ expression background and growth factor context. In testing model predictions, we demonstrated that PTPRJ suppressed MET-induced cell cell proliferation via regulation of a HER3/AKT signaling axis that stabilized PTPRJ expression through an unanticipated feedback mechanism. We also found that PTPRJ regulated HSC3 cell migration via JNK signaling that was preferentially activated by MET. Our results identify new regulatory nodes through which PTPRJ influences cancer cell phenotypes and demonstrates that these processes preferentially occur in the context of distinct RTK activation states.

systems biology↗

bioRxiv2026

Rational design of a protein-protein interaction inhibitor that activates Protein Tyrosine Phosphatase 1B.

Reversible inactivation of protein tyrosine phosphatases by reactive oxygen species (ROS) is essential to the phosphorylation of growth factor receptors. An important outcome of the inactivation of protein tyrosine phosphatase 1B (PTP1B) by ROS involves the conformational change of its phosphotyrosine binding loop which adopts a solvent exposed position in its oxidized form. We previously demonstrated that 14-3-3{zeta} binds to the phosphotyrosine binding loop of the oxidized form of PTP1B. Using a rational approach, we developed a unique protein-protein interaction (PPI) inhibitor peptide derived from the phosphotyrosine binding loop of PTP1B designed to disrupt the interaction between PTP1B and the 14-3-3{zeta}-complex. Exploiting this cell-permeable peptide, we showed decreased association between PTP1B and the 14-3-3{zeta}-complex in cells treated with epidermal growth factor (EGF). We also demonstrated that preventing the association of this 14-3-3{zeta}-complex to PTP1B deterred oxidation and inactivation of PTP1B following EGF receptor (EGFR) activation and generation of ROS. Treating cells with our PPI inhibitor decreased EGFR phosphorylation on PTP1B-specific sites. Furthermore, treating EGFR-driven epidermal cancer cells with our PPI inhibitor also significantly inhibited colony formation and cell viability, consitent with increased activation of PTP1B. These data highlight the ability of PTP1B to downregulate critical signaling pathways in cancer when activated using peptide drugs such as our protein-protein interaction inhibitor. We anticipate that preventing or destabilizing the reversible oxidation of other members of the protein tyrosine phosphatase superfamily using PPI inhibitors may offer a foundation for a broad therapeutic approach to rectify dysregulated signaling pathways in vivo. Significance StatementLimited understanding of redox mechanisms regulating PTP catalytic activity is a major knowledge gap that has hampered our efforts to develop activation strategies. In its reversibly oxidized and inactivated form, conformational changes of PTP1B influence its association with regulatory proteins. We demonstrate that designing a cell-permeable peptide based on a loop of PTP1B that becomes exposed during oxidation can block its interaction with the 14-3-3{zeta}-multiprotein complex and activate the phosphatase. Moreover, activating PTP1B using our protein-protein interaction inhibitor peptide decreases the phosphorylation of its substrate EGFR and decreases the effectiveness of cancer cells to form colonies. This study provides important insights into the therapeutic potential of protein-protein interaction inhibitors that regulate the redox cycle of PTPs to reestablish physiological signaling.

biochemistry↗

bioRxiv2025

PTPRJ-Targeting Peptide Agonist Induces Broad Cellular Signaling Perturbations and DNA Damage in Lung Cancer Cells

Receptor protein tyrosine phosphatases (RPTPs) are key regulators of cell signaling. However, their study and therapeutic targeting have been limited by the lack of known natural ligands or selective agonists, as well as an incomplete understanding of their structure-function relationships. Nonetheless, receptor homodimerization has been shown to suppress RPTP catalytic activity by restricting substrate access, offering a promising strategy for examining and modulating their function. Our previous work on PTPRJ, a member of the RPTP family, showed that its transmembrane domain regulates homodimerization, thereby controlling access to receptor tyrosine kinase (RTK) substrates and their phosphorylation levels. We also developed peptides that disrupt this dimerization, thereby inhibiting RTK phosphorylation and reducing cancer cell migration. These peptides were then engineered for selective, pH-sensitive insertion into the acidic tumor microenvironment to enhance efficacy while limiting off-target effects. Yet how broadly PTPRJ activation reshapes the phosphotyrosine landscape and whether those changes yield coherent cellular phenotypes remains unclear. In this study, we employed tyrosine phosphoproteomics, immunoblotting, immunofluorescence, and functional assays to assess the global impact of our lead peptide candidate, Hybrid 7, in A549 lung cancer cells that endogenously express PTPRJ. We find that Hybrid 7 decreases EGFR phosphorylation and selectively reduces phosphorylation across additional RTKs and motility adaptors, producing strong inhibition of EGF-driven migration and reduced proliferation. Hybrid 7 also elevates reactive oxygen species and DNA damage, and enforces CDK1-dependent G2/M arrest, indicating a primarily cytostatic, checkpoint-mediated response. These findings highlight the potential of RPTP-targeting peptides as valuable tools for dissecting RPTP function and as possible therapeutic agents capable of modulating key oncogenic pathways and inhibiting cancer progression.

biochemistry↗

bioRxiv2025

Flow transports extracellular lipid-anchored proteins across the surface of living COS-7 cells

The rapid diffusion of membrane lipids and membrane proteins in living cell plasma membranes demonstrates that the membrane is fluid. However, motion of membrane molecules is inhibited on one side by the cytoskeletal mesh, and on the other by the glycocalyx, a layer of proteoglycans with long polysaccharide chains that covers the membrane surface. A variety of biological fluid flows (including blood circulation, cilia-driven flows, and swimming motion of microorganisms) apply shear stress to cell surfaces. Cell responses to these flows govern important physiological processes such as blood pressure and immune activation. The presence of the glycocalyx is generally thought to shield cell membranes from shear stress that arises from flow. However, here we show that two different proteins, each attached by a lipid anchor to the extracellular membrane surface of living COS-7 cells, formed reversible, cell-wide concentration gradients in the direction of applied flow. Protein redistribution occurred within minutes after we applied shear stress levels commonly found in animal cardiovascular systems. The dynamic and spatial features of these gradients were consistent with passive transport by flow. Passive flow transport could be a general mechanism for spatial organization of membrane proteins. This mechanism may explain protein patterning previously observed on flow-exposed cells, and potentially forms an initial step in flow sensing.

biophysics↗

bioRxiv2025

Shear Stress Induces Concentration Gradient Distributions of Membrane Proteins in Live Cells

Cells sense and respond to fluid shear stress. Cell surfaces are exposed to flow, yet the influence of shear stress on the behavior of plasma membrane proteins remains unclear. Here we show that extracellular flow induces the gradient distribution of cell membrane proteins with increasing concentration toward the downstream direction of the flow. Shear stress at 10-30 dynes/cm2 caused formation of concentration gradients of both GPI-anchored proteins and transmembrane proteins, including integrin{beta}1, E-cadherin and the insulin receptor in Xenopus XTC cells. Using single-molecule live-cell imaging, we found that GPI-anchored T-cadherin molecules are dragged along the direction of flow under shear stress. In addition, shear stress induced concentration gradients of membrane proteins in COS-7 cells and human umbilical vein endothelial cells (HUVECs). Our findings suggest that external flow directly transports membrane proteins, establishing concentration gradients that may contribute to the cellular flow-sensing mechanism.

biophysics↗

bioRxiv2025

Deep learning-based joint sequence-structure de novo membrane protein design

Deep learning has revolutionized soluble protein design, yet de novo transmembrane (TM) protein engineering remains hindered by scarce structural data, complex membrane-specific interactions and conformational dynamics. We developed TMDiffusion (TMDF), a joint all-heavy-atom sequence-structure diffusion model trained to capture the full interaction diversity of natural TM proteins, including weak and polar contact networks. TMDF designs diverse TM architectures--associating domains, inhibitors, and conformational switches--in a single step, achieving >70% experimental success. A crystal structure of designed proteins matches predictions with atomic accuracy. Leveraging TMDF, we built synthetic single-pass receptors whose de novo TM domains toggle between conformations, enabling precise control of signalling outputs consistent with predicted equilibria. These results show that membrane-adapted DL models can accurately encode and program TM association energetics and conformations. TMDF establishes a general framework for bottom-up design of TM proteins with programmable functions, advancing both mechanistic studies of membrane proteins and development of next-generation therapeutics.

biophysics↗

bioRxiv2023

Targeted Acidosis Mediated Delivery of Antigenic MHC-Binding Peptides

Cytotoxic T lymphocytes are the primary effector immune cells responsible for protection against cancer, as they target peptide neoantigens presented through the major histocompatibility complex (MHC) on cancer cells, leading to cell death. Targeting peptide-MHC (pMHC) complexes offers a promising strategy for immunotherapy due to its specificity and effectiveness against cancer. In this work, we exploit the acidic tumor micro-environment to selectively deliver antigenic peptides to cancer cells using pH(low) insertion peptides (pHLIP). We demonstrated that the delivery of MHC binding peptides directly to the cytoplasm of melanoma cells resulted in the presentation of antigenic peptides on MHC, and subsequent activation of T cells. This work highlights the potential of pHLIP as a vehicle for targeted delivery of antigenic peptides and their presentation via MHC-bound complexes on cancer cell surfaces for activation of T cells with implications for enhancing anti-cancer immunotherapy.

cancer biology↗

bioRxiv2021

Selective Display of a Chemoattractant Agonist on Cancer Cells Activates the Formyl Peptide Receptor 1 on Immune Cells

Current immunotherapeutics often work by directing components of the immune system to recognize biomarkers on the surface of cancer cells to generate an immune response. However, variable changes in biomarker distribution and expression can result in uneven patient response. The development of a more universal tumor-homing strategy has the potential to improve selectivity and extend therapy to cancers with decreased expression or absence of specific biomarkers. Here, we designed a bifunctional agent that exploits the inherent acidic microenvironment of most solid tumors to selectively graft the surface of cancer cells with a formyl peptide receptor ligand (FPRL). Our approach is based on the pH(Low) Insertion Peptide (pHLIP), a unique peptide that selectively targets tumors in vivo by anchoring onto cancer cells in a pH-dependent manner. We establish that selectively remodeling cancer cells with a pHLIP-based FPRL activates formyl peptide receptors on recruited immune cells, potentially initiating an immune response towards tumors.

immunology↗

bioRxiv2019

pH-Dependent Grafting of Cancer Cells with Antigenic Epitopes Promotes Selective Antibody-Mediated Cytotoxicity

A growing class of immunotherapeutic agents work by redirecting components of the immune system to recognize specific markers on the surface of cancer cells and initiate a selective immune response. However, such immunotherapeutic modalities will remain confined to a relatively small subgroup of patients until two major hurdles are overcome: (1) the specific targeting of cancer cells relative to healthy cells, and (2) the lack of common targetable tumor biomarkers among all patients. Here, we designed a unique class of agents that exploit the inherent acidic microenvironment of solid tumors to selectively graft the surface of cancer cells with immuno-engager epitopes for directed destruction by components of the immune system. Specifically, conjugates were assembled using an antigen that recruit antibodies present in human serum, and the pH(Low) Insertion Peptide (pHLIP), a unique peptide that selectively target tumors in vivo by anchoring onto cancer cell surfaces in a pH-dependent manner. We established that conjugates can recruit antibodies from human serum to the surface of cancer cells, and induce complement-dependent and antibody-dependent cellular cytotoxicity by peripheral blood mononuclear cells and also an engineered NK cell line. These results suggest that these agents have the potential to be applicable to treating a wide range of solid tumors and to circumvent the problem of narrow windows of selectivity.

immunology↗

bioRxiv2019

Disrupting the Transmembrane Domain Oligomerization of Protein Tyrosine Phosphatase Receptor J Promotes its Activity in Cancer Cells

Despite the critical regulatory roles that receptor protein tyrosine phosphatases (RPTP) play in mammalian signal transduction, the detailed structural basis for the regulation of their catalytic activity is not fully understood, nor are they generally therapeutically targetable. It is due, in part, to the lack of known natural ligands or selective agonists. In contrast to conventional structure-function relationship for receptor tyrosine kinases (RTKs), the activity of RPTPs has been reported to be suppressed by dimerization, which may prevent their access to their RTK substrates. We report here that: (i) homodimerization of PTPRJ (also known as DEP-1) is regulated by specific transmembrane (TM) residues, and (ii) disrupting these interactions can destabilize full-length PTPRJ homodimerization in cells, reduce the phosphorylation of EGFR (a known substrate) and downstream signaling effectors, antagonize EGFR-driven cell phenotypes, and promote substrate access. We demonstrate these points in human cancer cells using both mutational studies and through the identification of a peptide designed to bind to the PTPRJ TM domain. This peptide is the first example of such allosteric agonist of RPTPs. This study, therefore, provides not only fundamental structure-function insights on how PTPRJ activity is tuned by TM interactions in cells but also opportunities to develop a unique class of agents that could be used as tools to probe RPTPs signaling regulating mechanisms or for therapeutic purposes in cancers driven by RTK signaling.

biochemistry↗