Periodic Reporting for period 4 - IM-ID (Defining the intrinsic transcriptional programs and the microenvironmental signals tailoring lung Interstitial Macrophage IDentity)
Reporting period: 2023-07-01 to 2024-12-31
Resident tissue macrophages (RTM) are present in most tissues and are recognized as an integral part of the tissues, where they play key roles in development, homeostasis, metabolism and repair. The diversity and identity (ID) of RTM is thought to rely on signals they receive from their microenvironment (i.e. the local niche), which trigger activation of specific transcription factors and differentiation programs, thus tailoring a particular identity that fulfills tissue-specific functions. We have previously identified lung interstitial macrophages (IM) as crucial regulators of lung tissue homeostasis at steady-state. However, they have been mainly investigated as a bulk population in functional studies. The ERC grant “IM-ID” aims to define the identity of IM at the highest resolution, model the differentiation of IM from monocytes using an innovative transgenic mouse model allowing IM niche depletion and refilling in vivo, and thereby investigate the intrinsic transcriptional programs and the niche-derived signals tailoring lung IM ID and sustaining lung homeostasis. This project will increase our understanding of the basic mechanisms underlying the fine-tuning of tolerogenic IM and will thus provide robust foundations for novel IM-targeted approaches promoting health and preventing lung diseases in which IM (dys)functions have been implicated.
The lungs, as the primary interface between the body and the external environment, are continually exposed to airborne particles, allergens, pathogens, and pollutants. The immune system within the lungs must carefully balance immune responses to protect against harmful threats while avoiding unnecessary reactions to harmless environmental components. When this balance is disrupted, immune dysfunction can lead to chronic respiratory diseases.
Our previous research identified a population of lung-resident immune cells, known as interstitial macrophages (IM), which play a crucial role in regulating immune responses in the lungs. However, at the start of this ERC-funded project, IM were only rudimentarily characterized, and their diversity, functional specialization, and mechanisms of regulation remained largely unknown.
Deciphering the Heterogeneity of Interstitial Macrophages
In the first phase of the project, we employed high-dimensional single-cell RNA-sequencing to uncover the diversity of lung IM. This revealed that IM are not a uniform cell population but instead consist of two functionally distinct subsets: CD206^hi IM and CD206^low IM. These two subpopulations differ in their origin, morphology, function, and localization within the lung. Given these fundamental differences, it is now essential for future research to consider them as separate entities when studying lung immunity and pathology. This discovery was published in Nature Communications in 2019 (Schyns et al., Nat Commun, 2019).
Unraveling the Molecular Regulation of IM Development and Function
A key challenge in understanding IM biology is identifying the molecular mechanisms that govern their development and differentiation. To address this, we generated a novel transgenic mouse model enabling the complete depletion of IM. Using this model, we demonstrated that once IM are depleted, they are rapidly replenished by incoming monocytes, which differentiate into IM. By performing single-cell RNA-sequencing at different time points after depletion, we provided the first high-resolution map of the IM differentiation process. We identified that MafB was essential for the differentiation of both IM subsets, while c-Maf played a role in the development of CD206^hi IM. We also discovered that blood monocytes retain the capacity to proliferate in tissues, thereby forming a reservoir that gives rise to IM. These findings, published in Nature Immunology in 2023 (Vanneste et al., Nat Immunol, 2023).
Identifying Tissue-Derived Signals that Shape IM Identity
In this part of the project, we found that endothelial cells release transforming growth factor-beta 1 (TGF-β1), which plays a critical role in shaping IM development and identity. When IM were unable to respond to TGF-β1, they underwent drastic alterations in numbers, phenotype, and localization. Notably, this disruption led to the development of age-related abnormalities in the lung, highlighting the importance of IM in maintaining lung integrity and pulmonary homeostasis. These findings are currently in press in Science Immunology. Moreover, ongoing investigations suggest that nerve endings, in addition to endothelial cells, can also release signals that direct the functional specialization of one IM subset. These findings open new avenues for exploring neuro-immune interactions in lung health and disease.
Beyond generating fundamental knowledge on lung IM, this ERC project has also provided valuable tools for the scientific community. Indeed, we developed multiple transgenic mouse models that allow for precise targeting and manipulation of IM in vivo. These models will serve as essential resources for future studies aimed at dissecting IM biology and their role in various respiratory diseases.
The discoveries made throughout this ERC-funded research have significantly advanced our understanding of lung macrophages and their role in immune regulation. These findings have been widely disseminated through high-impact publications, international conferences (European Congress of Immunology; World Immune Regulation meeting; Keystone symposium), and invited presentations in research Institutes (Gustave Roussy Paris, Inserm Toulouse, Edinburgh University). This project lays the groundwork for translational applications aimed at harnessing macrophage functions for therapeutic benefit in the context of chronic respiratory diseases.
Our previous research identified a population of lung-resident immune cells, known as interstitial macrophages (IM), which play a crucial role in regulating immune responses in the lungs. However, at the start of this ERC-funded project, IM were only rudimentarily characterized, and their diversity, functional specialization, and mechanisms of regulation remained largely unknown.
Deciphering the Heterogeneity of Interstitial Macrophages
In the first phase of the project, we employed high-dimensional single-cell RNA-sequencing to uncover the diversity of lung IM. This revealed that IM are not a uniform cell population but instead consist of two functionally distinct subsets: CD206^hi IM and CD206^low IM. These two subpopulations differ in their origin, morphology, function, and localization within the lung. Given these fundamental differences, it is now essential for future research to consider them as separate entities when studying lung immunity and pathology. This discovery was published in Nature Communications in 2019 (Schyns et al., Nat Commun, 2019).
Unraveling the Molecular Regulation of IM Development and Function
A key challenge in understanding IM biology is identifying the molecular mechanisms that govern their development and differentiation. To address this, we generated a novel transgenic mouse model enabling the complete depletion of IM. Using this model, we demonstrated that once IM are depleted, they are rapidly replenished by incoming monocytes, which differentiate into IM. By performing single-cell RNA-sequencing at different time points after depletion, we provided the first high-resolution map of the IM differentiation process. We identified that MafB was essential for the differentiation of both IM subsets, while c-Maf played a role in the development of CD206^hi IM. We also discovered that blood monocytes retain the capacity to proliferate in tissues, thereby forming a reservoir that gives rise to IM. These findings, published in Nature Immunology in 2023 (Vanneste et al., Nat Immunol, 2023).
Identifying Tissue-Derived Signals that Shape IM Identity
In this part of the project, we found that endothelial cells release transforming growth factor-beta 1 (TGF-β1), which plays a critical role in shaping IM development and identity. When IM were unable to respond to TGF-β1, they underwent drastic alterations in numbers, phenotype, and localization. Notably, this disruption led to the development of age-related abnormalities in the lung, highlighting the importance of IM in maintaining lung integrity and pulmonary homeostasis. These findings are currently in press in Science Immunology. Moreover, ongoing investigations suggest that nerve endings, in addition to endothelial cells, can also release signals that direct the functional specialization of one IM subset. These findings open new avenues for exploring neuro-immune interactions in lung health and disease.
Beyond generating fundamental knowledge on lung IM, this ERC project has also provided valuable tools for the scientific community. Indeed, we developed multiple transgenic mouse models that allow for precise targeting and manipulation of IM in vivo. These models will serve as essential resources for future studies aimed at dissecting IM biology and their role in various respiratory diseases.
The discoveries made throughout this ERC-funded research have significantly advanced our understanding of lung macrophages and their role in immune regulation. These findings have been widely disseminated through high-impact publications, international conferences (European Congress of Immunology; World Immune Regulation meeting; Keystone symposium), and invited presentations in research Institutes (Gustave Roussy Paris, Inserm Toulouse, Edinburgh University). This project lays the groundwork for translational applications aimed at harnessing macrophage functions for therapeutic benefit in the context of chronic respiratory diseases.
This ERC project has significantly advanced our understanding of lung macrophages, moving beyond previous knowledge in several key areas:
- Revealing IM heterogeneity: our research demonstrated that IM comprise two distinct subsets, each with different functions, origins, and localizations. This paradigm shift redefines how IM should be studied in lung immunity and pathology.
- Uncovering molecular regulators of IM differentiation: we identified MafB as a key driver of IM differentiation and c-Maf as essential for CD206^hi IM subset specification, establishing a molecular framework for IM lineage commitment.
- Redefining monocyte potential: the project revealed that monocytes can proliferate in tissues and generate a pool of local precursors for IM development, contradicting the longstanding view that monocytes are terminally differentiated upon tissue entry.
- Discovering niche-derived signals regulating IM: we demonstrated that TGF-β1 from endothelial cells is crucial for IM maintenance, and its absence leads to premature lung aging.
- Developing innovative transgenic mouse models: to enable further studies, we engineered novel transgenic mouse models allowing for selective depletion and manipulation of IM in vivo. These models will be invaluable for researchers investigating macrophage development and function.
- Potential therapeutic applications: By identifying the key molecular players and environmental cues regulating IM, this research lays the groundwork for macrophage-targeted therapies that could be leveraged to treat respiratory diseases such as asthma, fibrosis, and aging-related lung dysfunction.
- Revealing IM heterogeneity: our research demonstrated that IM comprise two distinct subsets, each with different functions, origins, and localizations. This paradigm shift redefines how IM should be studied in lung immunity and pathology.
- Uncovering molecular regulators of IM differentiation: we identified MafB as a key driver of IM differentiation and c-Maf as essential for CD206^hi IM subset specification, establishing a molecular framework for IM lineage commitment.
- Redefining monocyte potential: the project revealed that monocytes can proliferate in tissues and generate a pool of local precursors for IM development, contradicting the longstanding view that monocytes are terminally differentiated upon tissue entry.
- Discovering niche-derived signals regulating IM: we demonstrated that TGF-β1 from endothelial cells is crucial for IM maintenance, and its absence leads to premature lung aging.
- Developing innovative transgenic mouse models: to enable further studies, we engineered novel transgenic mouse models allowing for selective depletion and manipulation of IM in vivo. These models will be invaluable for researchers investigating macrophage development and function.
- Potential therapeutic applications: By identifying the key molecular players and environmental cues regulating IM, this research lays the groundwork for macrophage-targeted therapies that could be leveraged to treat respiratory diseases such as asthma, fibrosis, and aging-related lung dysfunction.