Multi-omic immune phenotyping of circulating and resident immune cells in human infective endocarditis

Rainer Kaiser (München)1, C. Gold (München)1, M. Joppich (München)1, R. Escaig (München)1, A. Droste zu Senden (München)1, A. Akhalkatsi (München)1, C. Spinner (München)2, J. Erber (München)2, S. Saha (München)1, C. Hagl (München)3, S. Massberg (München)1, K. Stark (München)1, L. Nicolai (München)1, K. Pekayvaz (München)1

1LMU Klinikum der Universität München Medizinische Klinik und Poliklinik I München, Deutschland; 2Klinikum rechts der Isar 2. Medizinische Klinik München, Deutschland; 3LMU Klinikum der Universität München Herzchirurgische Klinik und Poliklinik München, Deutschland



Bacterial infection of the heart valves, infective endocarditis (IE), is characterized by local vegetation formation and severe systemic complications associated with high mortality. Clinical symptoms are mostly unspecific, and definitive diagnosis is often delayed until local or systemic complications such as valvular destruction, abscess formation or systemic thromboembolisms occur. Current therapeutic approaches are limited to antibiotic treatment and cardiac surgery. Thus far, pathophysiological knowledge is mainly derived from rodent models, while the complex interplay between the causing pathogen, immune populations and the coagulation system in humans are however insufficiently understood.


In this multicentric, prospective translational study, we longitudinally study the local and systemic immune response in patients with IE according to the modified Duke criteria (n=32) using single-cell transcriptomic, proteomic and flow cytometry approaches. We compare blood samples of endocarditis patients with healthy controls (n=45) as well as an independent, prospectively enrolled cohort of patients with acute non-cardiac bacterial infection (n=28), comprising a total of > 100 individuals. In a subgroup of patients requiring cardiac surgery, we use CD45+ cell enrichment by flow cytometry and subsequent single-cell RNA sequencing (scRNAseq) to map transcriptomic phenotypes in immune cells infiltrating the infected valve. We integrate these data with clinical parameters and plasma proteomics to comprehensively immunophenotype infective endocarditis.


We observed early neutrophilia and leukocytosis in IE patients, which resolved upon antibiotic and surgical treatment. Other leukocyte subsets did not show differential relative abundance compared to healthy controls and patients with extra-cardiac bacterial infection. Circulating neutrophils from IE patients upregulated proinflammatory cytokines and microbicidal factors at protein level, while as plasma proteomics reveals an early signature characterized by activation of the complement system, multi-level coagulation factors and antimicrobial proteins. Further, we detect an endocarditis-specific upregulation of immunothrombosis-related, proinflammatory transcription programs in lymphoid cells using scRNAseq of over 120,000 peripheral blood mononuclear cells (PBMCs) using state-of-the-art bioinformatic tools such as multi-omic factor analysis and the novel method FlowSet. Finally, performing scRNAseq of leukocytes derived from surgically resected valves, we find myeloid influx of both pro-inflammatory monocyte subsets, transcriptional re-programming of resident macrophages as well as valvular expansion of bactericidal neutrophil subsets, promoting vicious, self-sustaining circle ultimately leading to valvular destruction.


Our study provides the first comprehensive and holistic phenotyping approach to both local and systemic immune response in IE patients. We provide deep insights into pathogen-induced adaptations in patient-derived resident and circulating immune cells and an upregulation of immunothrombotic pathways specifically in innate immune cells, which may explain the complex clinical picture of endocarditis. Our study therefore provides a framework for a deeper pathophysiological understanding of IE and may aid in the development of both diagnostic and novel therapeutic approaches towards this ferocious and deadly disease.

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