Periodic Reporting for period 4 - DDRMac (DNA Damage Response-instructed Macrophage Differentiation in Granulomatous Diseases)
Période du rapport: 2023-10-01 au 2025-06-30
Macrophages are the most numerous immune cells in our tissues. They control both tissue health as well as respond to environmental pathogens. Macrophages have multiple functions including the removal of dead cells to keep tissues healthy, fighting invading pathogens by either ‘eating them’ or signaling to other immune cells, and helping with tissue regeneration after inflammation to facilitate a return to a state of health. Macrophages are thus part of a broader network of tissue immune cells that are there to maintain health. When macrophages are inappropriately activated they may act as if an invading pathogen is there and chronically maintain an inflammatory state. This leads to chronic inflammatory diseases, such as autoimmune diseases (like rheumatoid arthritis or systemic lupus erythematosus) and granulomatous diseases (like Crohn’s disease and sarcoidosis). These affect millions of young people worldwide and run a chronic course, meaning that those affected suffer for decades. Current treatments are only partly effective and we currently don’t have many treatments directed against macrophages. Understanding how macrophages lead to chronic inflammation may help us devise effective treatments, however our current understanding is very limited.
In this project, we aimed to explore the hypothesis that the way macrophages respond to genotoxic stress, in other words stress to our genetic material (DNA), may be a key pathway that leads to chronic inflammation. Genotoxic stress arises when our DNA is damaged by environmental stressors, such as ultraviolet radiation, or when our ability to repair our DNA is reduced, as occurs in aging or cancer. We reasoned that genotoxic stress may further arise in inflammatory conditions, when immune cells try to proliferate and thus make several new copies of their DNA, while at the same time they face inflammatory signals in their microenvironment, such as pro-inflammatory cytokines, thus experiencing replication stress (i.e. stress occurring during replication of the DNA). Replication stress may lead to cell cycle arrest or cell death, but it may also lead to reprogramming of cellular differentiation and function. Reprogrammed macrophages may then fuel inflammatory responses.
DDRMac aimed to shed light to the pathways by which macrophages respond to genotoxic stress and to unravel how these responses may fuel chronic inflammatory diseases. The goal was to provide new knowledge that may be harnessed for the therapeutic targeting of macrophages in chronic inflammatory diseases and cancer.
In this project, we aimed to explore the hypothesis that the way macrophages respond to genotoxic stress, in other words stress to our genetic material (DNA), may be a key pathway that leads to chronic inflammation. Genotoxic stress arises when our DNA is damaged by environmental stressors, such as ultraviolet radiation, or when our ability to repair our DNA is reduced, as occurs in aging or cancer. We reasoned that genotoxic stress may further arise in inflammatory conditions, when immune cells try to proliferate and thus make several new copies of their DNA, while at the same time they face inflammatory signals in their microenvironment, such as pro-inflammatory cytokines, thus experiencing replication stress (i.e. stress occurring during replication of the DNA). Replication stress may lead to cell cycle arrest or cell death, but it may also lead to reprogramming of cellular differentiation and function. Reprogrammed macrophages may then fuel inflammatory responses.
DDRMac aimed to shed light to the pathways by which macrophages respond to genotoxic stress and to unravel how these responses may fuel chronic inflammatory diseases. The goal was to provide new knowledge that may be harnessed for the therapeutic targeting of macrophages in chronic inflammatory diseases and cancer.
To explore how macrophages responses to genotoxic stress may rewire their genetic programs and change their functions, we interrogated the role of the DNA Damage Response, or DDR in macrophages. Using genetic models to target DDR-related molecules specifically in macrophages, we analysed the role of the DDR in macrophages of multiple tissues, including the lung, intestine, joints, bone and liver, both in health and during the development of inflammatory diseases, such as intestinal or joint inflammation.
Our work revealed that the DDR was important for the differentiation and function of tissue macrophages both in health and during inflammation, but not all tissue macrophages were equal in their dependence on the DDR for their function. The conceptual framework of these studies was published in two articles (Kasapi A, Triantafyllopoulou A. Genotoxic stress signalling as a driver of macrophage diversity. Cell Stress 2022 Feb 14;6(3):30-44. and Fabry LAR, Triantafyllopoulou A. Der Rolle der DNA-Schadensantwort bei granulomatösen Erkrankungen [The role of the response to DNA damage in granulomatous diseases]. Z Rheumatol. 2022 Dec;81(10):881-887).
In addition to our investigation of granulomatous inflammatory diseases, we explored the pathways that control macrophage differentiation and function in autoimmune diseases, such as systemic lupus erythematosus (SLE). Around five million people worldwide, mostly young women, are affected by SLE, which can lead to kidney inflammation (lupus nephritis). Lupus nephritis is in many patients difficult to treat and can lead to kidney failure and thus dialysis.In SLE, endogenous DNA damage can lead to the release of damage-associated molecular patterns leading to chronic stimulation of our immune system by endogenous nucleic acids. This leads to the development of autoantibodies against self nucleic acids. Macrophages sense both nucleic acids and bind autoantibodies, leading to their activation. Activated macrophages fuel inflammation and tissue damage.We uncovered that a small, specialized group of tissue resident immune cells—known as innate lymphoid cells (ILCs) is activated in lupus via their surface receptor NKp46 and directly programs macrophages that are coming into the tissue from the bone marrow. This triggers an avalanche of effects that leads to lupus nephritis and subsequent severe tissue damage. Depleting NKp46-expressing ILC suppressed tissue damage.
To explore how ILC controlled macrophages we used single-cell RNA sequencing of the entire kidney as well as immune cells. scRNA-seq is a technique that allows to analyze in depth the program of individual cells and to explore their potential interactions. We found out that when NKp46 is activated, ILC increase their production of the protein GM-CSF, a growth factor that expands proinflammatory macrophages, causing severe tissue damage and the formation of scar tissue, known as fibrosis. Blocking the NKp46 receptor with antibodies or genetically deleting the receptor, suppressed kidney damage. A similar anti-inflammatory effect was observed when GM-CSF was blocked. These findings showed how a small population of innate lymphoid cells that reside in tissues, can sense stress induced by endogenous DNA damage and amplify inflammation by controlling proinflammatory macrophages. This work was published in the journal Nature (Biniaris-Georgallis SI, Aschman T, Stergioula K et al. Amplification of autoimmune organ damage by NKp46-activated ILC1. Nature 2024) and communicated to the public via a press release and an newspaper article (joint press release from the Charite and the MDC ‘Surprising mechanism of lupus kidney damage identified’, August 14, 2024. Interview by Adelheid Müller-Lissner titled ‘Immune disease Lupus: scientists from Berlin want to stop the self-destruction of the kidney’ was published online on the Tagespiegel, August 28, 2024).
Our work revealed that the DDR was important for the differentiation and function of tissue macrophages both in health and during inflammation, but not all tissue macrophages were equal in their dependence on the DDR for their function. The conceptual framework of these studies was published in two articles (Kasapi A, Triantafyllopoulou A. Genotoxic stress signalling as a driver of macrophage diversity. Cell Stress 2022 Feb 14;6(3):30-44. and Fabry LAR, Triantafyllopoulou A. Der Rolle der DNA-Schadensantwort bei granulomatösen Erkrankungen [The role of the response to DNA damage in granulomatous diseases]. Z Rheumatol. 2022 Dec;81(10):881-887).
In addition to our investigation of granulomatous inflammatory diseases, we explored the pathways that control macrophage differentiation and function in autoimmune diseases, such as systemic lupus erythematosus (SLE). Around five million people worldwide, mostly young women, are affected by SLE, which can lead to kidney inflammation (lupus nephritis). Lupus nephritis is in many patients difficult to treat and can lead to kidney failure and thus dialysis.In SLE, endogenous DNA damage can lead to the release of damage-associated molecular patterns leading to chronic stimulation of our immune system by endogenous nucleic acids. This leads to the development of autoantibodies against self nucleic acids. Macrophages sense both nucleic acids and bind autoantibodies, leading to their activation. Activated macrophages fuel inflammation and tissue damage.We uncovered that a small, specialized group of tissue resident immune cells—known as innate lymphoid cells (ILCs) is activated in lupus via their surface receptor NKp46 and directly programs macrophages that are coming into the tissue from the bone marrow. This triggers an avalanche of effects that leads to lupus nephritis and subsequent severe tissue damage. Depleting NKp46-expressing ILC suppressed tissue damage.
To explore how ILC controlled macrophages we used single-cell RNA sequencing of the entire kidney as well as immune cells. scRNA-seq is a technique that allows to analyze in depth the program of individual cells and to explore their potential interactions. We found out that when NKp46 is activated, ILC increase their production of the protein GM-CSF, a growth factor that expands proinflammatory macrophages, causing severe tissue damage and the formation of scar tissue, known as fibrosis. Blocking the NKp46 receptor with antibodies or genetically deleting the receptor, suppressed kidney damage. A similar anti-inflammatory effect was observed when GM-CSF was blocked. These findings showed how a small population of innate lymphoid cells that reside in tissues, can sense stress induced by endogenous DNA damage and amplify inflammation by controlling proinflammatory macrophages. This work was published in the journal Nature (Biniaris-Georgallis SI, Aschman T, Stergioula K et al. Amplification of autoimmune organ damage by NKp46-activated ILC1. Nature 2024) and communicated to the public via a press release and an newspaper article (joint press release from the Charite and the MDC ‘Surprising mechanism of lupus kidney damage identified’, August 14, 2024. Interview by Adelheid Müller-Lissner titled ‘Immune disease Lupus: scientists from Berlin want to stop the self-destruction of the kidney’ was published online on the Tagespiegel, August 28, 2024).
Our data are entirely novel, since the the pathways by which tissue immune cells sense and respond to endogenous DNA damage and communicate with each other to control or amplify inflammatory responses are largely unknown. Our work has revealed that macrophages respond to endogenous genotoxic stress both in health and in chronic inflammation and this response is crucial for their maintenance and function and ultimately for tissue health. Furthermore, we have unraveled a crucial role of tissue resident innate lymphoid cells in instructing macrophage programs and function, paving the ground for targeted therapies that can block receptors activating tissue resident innate lymphoid cells or their communication with tissue macrophages.