Evolutionary stability of antigenically escaping viruses

Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how this cost-benefit trade-off selects the mutation rate of viruses. Using a traveling wave model for the co-evolution of viruses and host immune systems in a finite population, we investigate how immunity affects the evolution of the mutation rate and other non-antigenic traits, such as virulence. We first show that the nature of the wave depends on how cross-reactive immune systems are, reconciling previous approaches. The immune-virus system behaves like a Fisher wave at low cross-reactivities, and like a fitness wave at high cross-reactivities. These regimes predict different outcomes for the evolution of non-antigenic traits. At low cross-reactivities, the evolutionarily stable strategy is to maximize the speed of the wave, implying a higher mutation rate and increased virulence. At large cross-reactivities, where our estimates place H3N2 influenza, the stable strategy is to increase the basic reproductive number, keeping the mutation rate to a minimum and virulence low

Imiter la réponse immunitaire humorale polyclonale : de l'association de deux anticorps monoclonaux aux productions oligoclonales

International audienceMonoclonal antibodies have revolutionized the treatment of many diseases, but their clinical effectiveness remains limited in some cases. Associations of antibodies binding to the same target (homo-combination) or to several different targets (hetero-combination), thereby mimicking a polyclonal humoral immune response, have demonstrated a therapeutic improvement in pre-clinical and clinical trials, mainly in the field of oncology and infectious diseases. The combinations increase the efficacy of the biological responses and override resistance mechanisms observed with antibody monotherapy. The most common method of formulating and administering antibody combinations is a separate formulation, with sequential injection of each antibody as individual drug substance. Alternatively, combined formulations are developed where the separately-produced antibodies are mixed before administration or produced simultaneously by a single cell line, or a mixture of cell lines as a polyclonal master cell bank. The regulation, the toxicity and the injection sequence of these oligoclonal antibody-based mixtures remain points to be clarified and optimized for a better therapeutic effect.Les anticorps monoclonaux ont révolutionné le traitement de nombreuses maladies mais leur efficacité clinique reste limitée dans certains cas. Des associations d'anticorps se liant à une même cible (homo-combinaisons) ou à plusieurs cibles différentes (hétéro-combinaisons), mimant ainsi une réponse immunitaire humorale polyclonale, ont conduit à une amélioration thérapeutique dans des essais précliniques et cliniques, essentiellement en cancérologie et en infectiologie. Ces combinaisons augmentent l'efficacité des réponses biologiques et court-circuitent les mécanismes de résistances observés lors d'une monothérapie par anticorps. Le procédé de formulation et d'administration des combinaisons d'anticorps le plus fréquent est une formulation séparée, avec injection séquentielle de chaque anticorps « principe actif ». Alternativement, se développent des formulations combinées, où les anticorps produits séparément sont mélangés avant administration, ou produits simultanément par une lignée cellulaire unique ou un mélange de lignées cellulaires correspondant à une master-bank 2 cellulaire polyclonale. La réglementation, la toxicité et la séquence d'injection des mélanges oligoclonaux restent des points à éclaircir et à optimiser pour un meilleur effet thérapeutique

A Renormalization Group Approach to Connect Discrete- and Continuous-Time Descriptions of Gaussian Processes

Discretization of continuous stochastic processes is needed to numerically simulate them or to infer models from experimental time series. However, depending on the nature of the process, the same discretization scheme, if not accurate enough, may perform very differently for the two tasks. Exact discretizations, which work equally well at any scale, are characterized by the property of invariance under coarse-graining. Motivated by this observation, we build an explicit Renormalization Group approach for Gaussian time series generated by auto-regressive models. We show that the RG fixed points correspond to discretizations of linear SDEs, and only come in the form of first order Markov processes or non-Markovian ones. This fact provides an alternative explanation of why standard delay-vector embedding procedures fail in reconstructing partially observed noise-driven systems. We also suggest a possible effective Markovian discretization for the inference of partially observed underdamped equilibrium processes based on the exploitation of the Einstein relation.Comment: 13 pages, 3 figures, 1 tabl

Building general Langevin models from discrete data sets

Many living and complex systems exhibit second order emergent dynamics. Limited experimental access to the configurational degrees of freedom results in data that appears to be generated by a non-Markovian process. This poses a challenge in the quantitative reconstruction of the model from experimental data, even in the simple case of equilibrium Langevin dynamics of Hamiltonian systems. We develop a novel Bayesian inference approach to learn the parameters of such stochastic effective models from discrete finite length trajectories. We first discuss the failure of naive inference approaches based on the estimation of derivatives through finite differences, regardless of the time resolution and the length of the sampled trajectories. We then derive, adopting higher order discretization schemes, maximum likelihood estimators for the model parameters that provide excellent results even with moderately long trajectories. We apply our method to second order models of collective motion and show that our results also hold in the presence of interactions.Comment: we correct previous inaccuracy about a reference; 29 pages, 9 figure

Design and selection of optimal ErbB-targeting bispecific antibodies in pancreatic cancer

The ErbB family of receptor tyrosine kinases is a primary target for small molecules and antibodies for pancreatic cancer treatment. Nonetheless, the current treatments for this tumor are not optimal due to lack of efficacy, resistance, or toxicity. Here, using the novel BiXAb™ tetravalent format platform, we generated bispecific antibodies against EGFR, HER2, or HER3 by considering rational epitope combinations. We then screened these bispecific antibodies and compared them with the parental single antibodies and antibody pair combinations. The screen readouts included measuring binding to the cognate receptors (mono and bispecificity), intracellular phosphorylation signaling, cell proliferation, apoptosis and receptor expression, and also immune system engagement assays (antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity). Among the 30 BiXAbs™ tested, we selected 3Patri-1Cetu-Fc, 3Patri-1Matu-Fc and 3Patri-2Trastu-Fc as lead candidates. The in vivo testing of these three highly efficient bispecific antibodies against EGFR and HER2 or HER3 in pre-clinical mouse models of pancreatic cancer showed deep antibody penetration in these dense tumors and robust tumor growth reduction. Application of such semi-rational/semi-empirical approach, which includes various immunological assays to compare pre-selected antibodies and their combinations with bispecific antibodies, represents the first attempt to identify potent bispecific antibodies against ErbB family members in pancreatic cancer

HER3 as biomarker and therapeutic target in pancreatic cancer: new insights in pertuzumab therapy in preclinical models.

International audienceThe anti-HER2 antibody pertuzumab inhibits HER2 dimerization and affects HER2/HER3 dimer formation and signaling. As HER3 and its ligand neuregulin are implicated in pancreatic tumorigenesis, we investigated whether HER3 expression could be a predictive biomarker of pertuzumab efficacy in HER2low-expressing pancreatic cancer. We correlated in vitro and in vivo HER3 expression and neuregulin dependency with the inhibitory effect of pertuzumab on cell viability and tumor progression. HER3 knockdown in BxPC-3 cells led to resistance to pertuzumab therapy. Pertuzumab treatment of HER3-expressing pancreatic cancer cells increased HER3 at the cell membrane, whereas the anti-HER3 monoclonal antibody 9F7-F11 down-regulated it. Both antibodies blocked HER3 and AKT phosphorylation and inhibited HER2/HER3 heterodimerization but affected differently HER2 and HER3 homodimers. The pertuzumab/9F7-F11 combination enhanced tumor inhibition and the median survival time in mice xenografted with HER3-expressing pancreatic cancer cells. Finally, HER2 and HER3 were co-expressed in 11% and HER3 alone in 27% of the 45 pancreatic ductal adenocarcinomas analyzed by immunohistochemistry. HER3 is essential for pertuzumab efficacy in HER2low-expressing pancreatic cancer and HER3 expression might be a predictive biomarker of pertuzumab efficacy in such cancers. Further studies in clinical samples are required to confirm these findings and the interest of combining anti-HER2 and anti-HER3 therapeutic antibodies

Imiter la réponse immunitaire humorale polyclonale

Les anticorps monoclonaux ont révolutionné le traitement de nombreuses maladies mais leur efficacité clinique reste limitée dans certains cas. Des associations d’anticorps se liant à une même cible (homo-combinaisons) ou à plusieurs cibles différentes (hétéro-combinaisons), mimant ainsi une réponse immunitaire humorale polyclonale, ont conduit à une amélioration thérapeutique dans des essais précliniques et cliniques, essentiellement en cancérologie et en infectiologie. Ces combinaisons augmentent l’efficacité des réponses biologiques et court-circuitent les mécanismes de résistances observés lors d’une monothérapie par anticorps. Le procédé de formulation et d’administration des combinaisons d’anticorps le plus fréquent est une formulation séparée, avec injection séquentielle de chaque anticorps « principe actif ». Alternativement, se développent des formulations combinées, où les anticorps produits séparément sont mélangés avant administration, ou produits simultanément par une lignée cellulaire unique ou un mélange de lignées cellulaires correspondant à une master-bank cellulaire polyclonale. La réglementation, la toxicité et la séquence d’injection des mélanges oligoclonaux restent des points à éclaircir et à optimiser pour un meilleur effet thérapeutique

Improving Biologics’ Effectiveness in Clinical Oncology: From the Combination of Two Monoclonal Antibodies to Oligoclonal Antibody Mixtures

International audienceMonoclonal antibodies have revolutionized the treatment of many diseases, but their clinical efficacy remains limited in some other cases. Pre-clinical and clinical trials have shown that combinations of antibodies that bind to the same target (homo-combinations) or to different targets (hetero-combinations) to mimic the polyclonal humoral immune response improve their therapeutic effects in cancer. The approval of the trastuzumab/pertuzumab combination for breast cancer and then of the ipilimumab/nivolumab combination for melanoma opened the way to novel antibody combinations or oligoclonal antibody mixtures as more effective biologics for cancer management. We found more than 300 phase II/III clinical trials on antibody combinations, with/without chemotherapy, radiotherapy, small molecules or vaccines, in the ClinicalTrials.gov database. Such combinations enhance the biological responses and bypass the resistance mechanisms observed with antibody monotherapy. Usually, such antibody combinations are administered sequentially as separate formulations. Combined formulations have also been developed in which separately produced antibodies are mixed before administration or are produced simultaneously in a single cell line or a single batch of different cell lines as a polyclonal master cell bank. The regulation, toxicity and injection sequence of these oligoclonal antibody mixtures still need to be addressed in order to optimize their delivery and their therapeutic effects

CD4 ligation excludes the Carma1-Bcl10-MALT1 complex from GM1-positive membrane rafts in CD3/CD28 activated T cells.

International audienceThe antibody 13B8.2, which is directed against the CDR3-like loop on the D1 domain of CD4, induces CD4/ZAP-70 reorganization and ceramide release in membrane rafts. Here, we investigated whether CD4/ZAP-70 compartmentalization could be mediated by an effect of 13B8.2 on the Carma1-Bcl10-MALT1 complex in membrane rafts. We report that treatment of CD3/CD28-activated Jurkat T cells with 13B8.2, but not rituximab, excluded Carma1-Bcl10-MALT1 proteins from GM1(+) membrane rafts and concomitantly decreased NF-κB activation. Fluorescence confocal imaging confirmed that Carma1-Bcl10 and Carma1-MALT1 co-patching, observed in GM1(+) membrane rafts following CD3/CD28 activation, were abrogated after a 24h-treatment with 13B8.2. The CD4/ZAP-70 compartmentalization in membrane rafts induced by 13B8.2 is thus related to Carma1-Bcl10-MALT1 raft exclusion