Biology subjects

Dagher, M.

Publications and source records attributed to Dagher, M..

3 recordsLinked to original sources

bioRxiv2025

Dynamical model and geometric insights in the discontinuity theory of immunity

The immune systems most basic task is to decide what is "self" and "non-self", but a precise definition of self versus non-self remains challenging. According to the discontinuity theory of immunity, effector responses depend on how quickly an antigenic stimulus changes: rapid change triggers an immune response, whereas gradual change fosters tolerance. We present a model of adaptive immune dynamics including T cells, Tregs and cytokines that reproduces the hallmarks of the discontinuity theory. The model allows for sharp discrimination between acute and chronic infections based on the growth rate of the immune challenge, and vaccination-like acute dynamics upon presentation of a bolus of immune challenge. We further show that the model behavior only depends on a handful of testable assumptions that we map to geometric constraints in phase space. This suggests that the model properties are generic and robust across alternative mechanistic details. We also examine the impact of multiple concurrent immune challenges in this model, and demonstrate the occurrence of dynamical antagonism, wherein, in some parameter regimes, slow-growing challenges hinder acute responses to fast-growing ones, with further counter-intuitive behaviors for sequential co-infections. Together, these results place the discontinuity theory on firm mathematical footing and encourage further investigation of interferences of multi-agent immune challenges, from chronic viral co-infections to cancer immunoediting.

systems biology↗

bioRxiv2024

A morphology and secretome map of pyroptosis

Pyroptosis represents one type of Programmed Cell Death (PCD). It is a form of inflammatory cell death that is canonically defined by caspase-1 cleavage and Gasdermin-mediated membrane pore formation. Caspase-1 initiates the inflammatory response (through IL-1{beta} processing), and the N-terminal cleaved fragment of Gasdermin D polymerizes at the cell periphery forming pores to secrete pro-inflammatory markers. Cell morphology also changes in pyroptosis, with nuclear condensation and membrane rupture. However, recent research challenges canon, revealing a more complex secretome and morphological response in pyroptosis, including overlapping molecular characterization with other forms of cell death, such as apoptosis. Here, we take a multimodal, systems biology approach to characterize pyroptosis. We treated human Peripheral Blood Mononuclear Cells (PBMCs) with 36 different combinations of stimuli to induce pyroptosis or apoptosis. We applied both secretome profiling (nELISA) and high-content fluorescence microscopy (Cell Painting). To differentiate apoptotic, pyroptotic and control cells, we used canonical secretome markers and modified our Cell Painting assay to mark the N-terminus of Gasdermin-D. We trained hundreds of machine learning (ML) models to reveal intricate morphology signatures of pyroptosis that implicate changes across many different organelles and predict levels of many pro-inflammatory markers. Overall, our analysis provides a detailed map of pyroptosis which includes overlapping and distinct connections with apoptosis revealed through a mechanistic link between cell morphology and cell secretome.

systems biology↗

bioRxiv2023

nELISA: A high-throughput, high-plex platform enables quantitative profiling of the secretome

We present the nELISA, a high-throughput, high-fidelity, and high-plex protein profiling platform. DNA oligonucleotides are used to pre-assemble antibody pairs on spectrally encoded microparticles and perform displacement-mediated detection. Spatial separation between non-cognate antibodies prevents the rise of reagent-driven cross-reactivity, while read-out is performed cost-efficiently and at high-throughput using flow cytometry. nELISA can measure both protein concentration and their post-translational modifications. We assembled an inflammatory panel of 191 targets that were multiplexed without cross-reactivity nor impact on performance vs 1-plex signals, with sensitivities as low as 0.1 pg/mL and measurements spanning 7 orders of magnitude. We then performed a large-scale inflammatory-secretome perturbation screen of peripheral blood mononuclear cells (PBMCs), with cytokines as both perturbagens and read-outs, measuring 7,392 samples and generating [~]1.4M protein data points in under a week; a significant advance in throughput compared to other highly multiplexed immunoassays. We uncovered 447 significant cytokine responses, including multiple putatively novel ones, that were conserved across donors and stimulation conditions. We validate nELISA for phenotypic screening, where its capacity to faithfully report hundreds of proteins make it a powerful tool across multiple stages of drug discovery.

bioengineering↗