Maëlick Brochut

We developed a high-dimensional spectral flow cytometry platform integrating AIM, RNA-FISH, transcription factor staining, and surface marker profiling for simultaneous functional and phenotypic characterization of antigen-specific CD4⁺ T cells. We applied this assay to analyze HIV- and CMV-specific CD4⁺ T-cell responses. Spectral cytometry improved marker resolution through extraction of RNA-FISH–induced autofluorescence and enabled highly specific identification of virus-specific cells using combined AIM⁺RNA⁺ gating. Although dual AIM combinations involving CD69, 4-1BB, and OX40 detected Th1-, Tfh-, and Th17/22-associated RNA⁺ cells, their sensitivity differed across cytokines. CD69 identified the majority of functional subsets, whereas 4-1BB and OX40 showed cytokine-dependent performance. The AIMFISH approach, combined with clustering analyses, revealed distinct functional and differentiation states of HIV-specific T helper cells associated with viremia and antiretroviral therapy. These findings delineate strengths and limitations of conventional AIM strategies and establish a flexible framework for the high-dimensional, single-cell cytometric profiling of pathogen-specific CD4⁺ T cell immunity.

Preclinical mouse models are critical for understanding the pathophysiological response to infections and developing treatment strategies for sepsis. In keeping with ethical values, researchers follow guidelines to minimize the suffering of the mice. Weight loss is a criteria used as a humane end point, but there is no official recommendation for a maximum weight loss leading to euthanasia. To evaluate whether the thresholds used in daily practice are optimal, we performed a comprehensive retrospective analysis of data generated over 10 years with > 2300 mice used in models of infection with Listeria monocytogenes, Streptococcus pneumoniae, Candida albicans and H1N1 influenza virus. Weight loss segregated mice that survived from those that did not. Statistical analyses revealed that lowering the weight loss thresholds used (none, 30% or 20%) would have increased mortality rates due to the sacrifice of mice that survived infections (p < 0.01–0.001). Power calculations showed high variability and reduction of power as weight loss thresholds approached 20% for S. pneumoniae and L. monocytogenes models. Hence, weight loss thresholds need to be adapted to each model of infection used in a laboratory. Overall, weight loss is a valuable predictor of mortality that contributes to the robustness of composite scores. To our knowledge, this is the most extensive study exploring the relationship between weight loss threshold and sepsis outcome. It underscores the importance of the infection-model-specific evaluation of weight loss for use in clinical scores defining humane endpoints to minimize mouse suffering without compromising statistical power and scientific objectives.

Patients admitted to the intensive care unit (ICU) often experience endotoxemia, nosocomial infections and sepsis. Polymorphonuclear and monocytic myeloid-derived suppressor cells (PMN-MDSCs and M-MDSCs) can have an important impact on the development of infectious diseases, but little is known about their potential predictive value in critically ill patients. Here, we used unsupervised flow cytometry analyses to quantify MDSC-like cells in healthy subjects challenged with endotoxin and in critically ill patients admitted to intensive care units and at risk of developing infections. Cells phenotypically similar to PMN-MDSCs and M-MDSCs increased after endotoxin challenge. Similar cells were elevated in patients at ICU admission and normalized at ICU discharge. A subpopulation of M-MDSC-like cells expressing intermediate levels of CD15 (CD15^int M-MDSCs) was associated with overall mortality (p = 0.02). Interestingly, the high abundance of PMN-MDSCs and CD15^int M-MDSCs was a good predictor of mortality (p = 0.0046 and 0.014), with area under the ROC curve for mortality of 0.70 (95% CI = 0.4–1.0) and 0.86 (0.62–1.0), respectively. Overall, our observations support the idea that MDSCs represent biomarkers for sepsis and that flow cytometry monitoring of MDSCs may be used to risk-stratify ICU patients for targeted therapy.