Immune cell dynamics deconvoluted by single-cell RNA sequencing in normothermic machine perfusion of the liver

Hautz, Theresa; Salcher, Stefan; Fodor, Margot; Sturm, Gregor; Ebner, Susanne; Mair, A.; Trebo, Manuel; Untergasser, Gerold; Sopper, Sieghart; Cardini, Benno; Martowicz, Agnieszka; Hofmann, Julia; Daum, Sophia; Kalb, Marcus; Resch, Thomas; Krendl, Felix J.; Weißenbacher, Annemarie; Otarashvili, Giorgi; Obrist, P.; Zelger, Bettina; Öfner, D.; Trajanoski, Zlatko; Troppmair, Jakob; Oberhuber, Rupert; Pircher, Andreas; Wolf, Dominik; Schneeberger, Stefan

doi:10.1038/s41467-023-37674-8

Cited by 31 publications

(23 citation statements)

References 98 publications

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“…MMP19 has also been implicated in M2 polarization [75], consistent with the anti-inflammatory signatures of the infected macrophage populations ( Figures 4J and S5E ). Cellular interactome analysis further predicted the anti-inflammatory status of neutrophils by a strong correlation in the CCL signaling pathway between neutrophils and M2-like macrophages, particularly through the Ccl3:Ccr1 axis ( Figures 5K-M and S6D ), an interaction predictive of neutrophil extravasation during E. faecalis infection[76]. Neutrophil extravasation is a vital event in immune responses to infections to ensure the survival of the host[7].…”

Section: Resultsmentioning

confidence: 99%

Decoding the complexity of delayed wound healing followingEnterococcus faecalisinfection

Celik,

Lee,

Tanoto

et al. 2023

Preprint

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Wound infections are highly prevalent, and can lead to delayed or failed healing, causing significant morbidity and adverse economic impacts. These infections occur in various contexts, including diabetic foot ulcers, burns, and surgical sites.Enterococcus faecalisis often found in persistent non-healing wounds, but its contribution to chronic wounds remains understudied. To address this, we employed single-cell RNA sequencing (scRNA-seq) on infected wounds in comparison to uninfected wounds in a mouse model. Examining over 23,000 cells, we created a comprehensive single-cell atlas that captures the cellular and transcriptomic landscape of these wounds. Our analysis revealed unique transcriptional and metabolic alterations in infected wounds, elucidating the distinct molecular changes associated with bacterial infection compared to the normal wound healing process. We identified dysregulated keratinocyte and fibroblast transcriptomes in response to infection, jointly contributing to an anti-inflammatory environment. Notably,E. faecalisinfection prompted a premature, incomplete epithelial-to-mesenchymal transition in keratinocytes. Additionally,E. faecalisinfection modulated M2-like macrophage polarization by inhibiting pro-inflammatory resolutionin vitro,in vivo,and in our scRNA-seq atlas. Furthermore, we discovered macrophage crosstalk with neutrophils, which regulates chemokine signaling pathways, while promoting anti-inflammatory interactions with endothelial cells. Overall, our findings offer new insights into the immunosuppressive role ofE. faecalisin wound infections.AUTHOR SUMMARYWound infections, including diabetic foot ulcers, burns, or surgical sites, often lead to prolonged healing and significant health and economic burdens. Among the bacteria implicated in these persistent wounds,Enterococcus faecalisremains a relatively enigmatic player. To unravel its role in non-healing wounds, we used single-cell RNA sequencing in a mouse model, scrutinizing over 23,000 cells to construct a comprehensive single-cell map of infected wounds compared to uninfected wounds. Our investigation revealed distinct genetic and metabolic alterations in infected wounds, in which infection resulted in a perturbed inflammatory environment delayed wound healing signatures. Specifically,E. faecalisinfection induces a premature and incomplete transition in keratinocytes, impeding their healing function. Furthermore, infection influences the behavior of immune cells like macrophages, affecting the body’s response to the infection. These findings not only shed light onE. faecalis’s role in delayed wound healing but also offer potential avenues for future treatments, providing valuable insights into the challenging realm of wound infections.

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Section: Resultsmentioning

confidence: 99%

Decoding the complexity of delayed wound healing followingEnterococcus faecalisinfection

Celik,

Lee,

Tanoto

et al. 2023

Preprint

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“…Single-cell RNA expression studies have revealed significant heterogeneity in the immune cell profiles in liver grafts, providing new therapeutic targets to prevent rejection [31 ▪▪ ]. Similar studies showed that normothermic machine perfusion shifts several immune cell populations in the donor liver [32 ▪▪ ] – inflammatory neutrophils take on an exhausted phenotype while tolerogenic monocytes increase. These shifts likely impact the donor liver's immunogenicity [33 ▪▪ ].…”

Section: The Pieces Of the Omics Puzzle And Their Influence On Liver ...mentioning

confidence: 95%

Improving liver transplant outcomes with transplant-omics and network biology

Scarpa

2023

Current Opinion in Organ Transplantation

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Purpose of review Molecular omics data is increasingly ubiquitous throughout medicine. In organ transplantation, recent large-scale research efforts are generating the ‘transplant-ome’ – the entire set of molecular omics data, including the genome, transcriptome, proteome, and metabolome. Importantly, early studies in anesthesiology have demonstrated how perioperative interventions alter molecular profiles in various patient populations. The next step for anesthesiologists and intensivists will be to tailor perioperative care to the transplant-ome of individual liver transplant patients. Recent findings In liver transplant patients, elements of the transplant-ome predict complications and point to novel interventions. Importantly, molecular profiles of both the donor organ and recipient contribute to this risk, and interventions like normothermic machine perfusion influence these profiles. As we can now measure various omics molecules simultaneously, we can begin to understand how these molecules interact to form molecular networks and emerging technologies offer noninvasive and continuous ways to measure these networks throughout the perioperative period. Molecules that regulate these networks are likely mediators of complications and actionable clinical targets throughout the perioperative period. Summary The transplant-ome can be used to tailor perioperative care to the individual liver transplant patient. Monitoring molecular networks continuously and noninvasively would provide new opportunities to optimize perioperative management.

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“…While the protective effect of NMP on ischemia/reperfusion injury occurs mainly when the perfusion is applied instead of conventional cold storage, as described in most initial studies, when combined with higher donor risk, steatosis, warm, or cold, NMP seems to have limited benefit (Figure 1). 9,11,12 The described changes in immunogenicity are, therefore, no surprise and were highlighted recently by the group from Innsbruck. Hautz et al 9 found a large, neutrophil-dominant leukocyte efflux into the perfusate during prolonged NMP.…”

mentioning

confidence: 91%

“… 9,11,12 The described changes in immunogenicity are, therefore, no surprise and were highlighted recently by the group from Innsbruck. Hautz et al 9 found a large, neutrophil-dominant leukocyte efflux into the perfusate during prolonged NMP. Authors further highlight a shift from a proinflammatory state toward a chronically activated and exhausted neutrophil phenotype, contributing to the general inflammatory response observed during NMP.…”

mentioning

confidence: 91%

“…Nonetheless, changes in the immunologic milieu have been shown during NMP as a downstream feature of ischemia/reperfusion injury (IRI), [7,8] suggesting a contributing role of NMP to elevated graft immunogenicity. A recent paper by Hautz et al [9] describes an increased predominance of neutrophils in the donor graft, with a shift from a proinflammatory state to a chronically activated/exhausted phenotype. In addition, the entire recipient cohort presented by Hann et al [5] consisted of candidates with retransplantation, a subgroup of liver transplant candidates with elevated immunological risk.…”

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confidence: 99%

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Reply: Acute rejection after transplantation of machine perfused livers—We have barely scratched the surface

et al. 2023

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We thank Liang et al [1] and Neil et al [2] for their letters regarding our recent meta-analysis on acute cellular rejection after liver transplantation with dynamic preservation versus static cold storage. [3] We appreciate the literature review conducted by Liang et al [1] although the mentioned studies were either excluded from our meta-analysis because they did not meet our inclusion criteria or were published after our literature search had already been completed. The authors are correct that Nasralla et al [4] state in their protocol that they will record biopsy-proven acute cellular rejection as a safety outcome; however, Extended Table 6, which summarizes all adverse events, only mentions "rejection".We commend the Birmingham group for their interesting work on retransplantation with "suboptimal liver grafts" after normothermic machine perfusion (NMP). [5] Hann and colleagues demonstrated an increased T-cell-mediated rejection after NMP, which poses relevant questions on the impact of normothermic preservation on immunogenicity. We agree that the DATA AVAILABILITYThe data, code, and other materials are available from the corresponding author upon reasonable request.

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Immune cell dynamics deconvoluted by single-cell RNA sequencing in normothermic machine perfusion of the liver

Cited by 31 publications

References 98 publications

Decoding the complexity of delayed wound healing followingEnterococcus faecalisinfection

Decoding the complexity of delayed wound healing followingEnterococcus faecalisinfection

Improving liver transplant outcomes with transplant-omics and network biology

Reply: Acute rejection after transplantation of machine perfused livers—We have barely scratched the surface

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