Abstract

Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is a common critical illness. Supportive therapy is still the main strategy for ALI/ARDS. Macrophages are the predominant immune cells in the lungs and play a pivotal role in maintaining homeostasis, regulating metabolism, and facilitating tissue repair. During ALI/ARDS, these versatile cells undergo polarization into distinct subtypes with significant variations in transcriptional profiles, developmental trajectory, phenotype, and functionality. This review discusses developments in the analysis of alveolar macrophage subtypes in the study of ALI/ARDS, and the potential value of targeting new macrophage subtypes in the diagnosis, prognostic evaluation, and treatment of ALI/ARDS.

1. Introduction

Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is a clinical syndrome characterized by uncontrolled inflammation [1], with a high incidence and mortality [2]. ALI/ARDS can be caused by a variety of direct or indirect factors, including pneumonia, gastric content aspiration, sepsis, trauma, pancreatitis, and blood transfusion [3, 4]. Excessive and uncontrolled inflammatory responses lead to epithelial and endothelial barrier damage, alveolar-capillary membrane dysfunction, increased vascular permeability, and pulmonary edema and hypoxemia [5, 6, 7].

Macrophages are the core immune cell population involved in the regulation of pulmonary inflammation. They release inflammatory cytokines, chemokines, and cytotoxic molecules such as interferon (IFN)-γ and tumor necrosis factor (TNF)-α, thereby activating neutrophils to cause a cytokine storm that leads to secondary pulmonary inflammation and tissue damage [8, 9, 10]. Macrophages are sentinel cells in the airways and alveoli, and when ALI/ARDS occurs, macrophages regulate the progression and regression of inflammation and maintain immune homeostasis in the lungs [11, 12].

Macrophages serve as the primary line of defense in innate immunity within the lungs and play a pivotal role in phagocytosis of pathogens and maintenance of immune homeostasis, which makes them a promising target for inhibiting progression of ALI/ARDS. Macrophages can be divided into different subtypes based on functional differences and expression of surface and intracellular markers. However, the results of current research on macrophage subtypes in ALI/ARDS are unclear. This review focuses on the methods of macrophage subtype analysis in ALI/ARDS, and the potential of targeting new macrophage subtypes in the diagnosis, prognostic evaluation, and treatment of ALI/ARDS.

2. Macrophage Subtypes

Macrophages, the principal effector cells defending the lungs against foreign stimuli, have essential roles in the pathogenesis of lung inflammation, and demonstrate notable heterogeneity and phenotypic alterations [13]. Pulmonary macrophages consist of two distinct types of macrophages situated in different anatomical locations: alveolar macrophages (AM) and interstitial macrophages (IM) [14]. AM constitute approximately 95% of the leukocytes in pulmonary tissue and serve as the primary defense against microorganisms [15]. They typically show high levels of Mer receptor tyrosine kinase (MerTK), Fc gamma receptor I (CD64), epithelial growth factor (EGF)-like module-containing mucin-like hormone receptor-like 1 (F4/80), sialic acid binding Ig-like lectin F (Siglec F), major histocompatibility complex II (MHC II), and CD11c, while demonstrating low levels of CD11b [16, 17, 18]. IM are situated within the connective tissue surrounding the bronchiolar airways and typically exhibit expression of CD64, CD11b, CD11c, major histocompatibility complex II, and MerTK. They play a pivotal role in inflammation, tissue damage, and repair [16]. AM are classified into two types: tissue-resident alveolar macrophages (TR-AM) and monocyte-derived alveolar macrophages (Mo-AM). TR-AM originate from the embryo and undergo self-renewal and proliferation in a quiescent state [19]. When the body encounters infection or injury, bone marrow or circulating monocytes rapidly migrate to the alveolar space and differentiate into Mo-AM, which facilitate inflammatory responses and eradication of pathogens. The recruited monocytes typically exhibit high expression of CD11b and lymphocyte antigen 6 family member C1 (Ly6C), while showing low expression of MerTK, CD64, and F4/80. Upon differentiation into Mo-AMs, these cells demonstrate high expression of CD64, CD11c, F4/80, and MerTK, with low expression of Siglec F [16, 17, 18, 20]. During the initial phase of the inflammatory response, the number of Mo-AM substantially surges, then decreases, thus leaving a small population of Mo-AM that persist after infection and exhibit phenotypic and functional similarities to TR-AM [14]. AM secrete substantial quantities of inflammatory factors, which in turn initiate a cascade effect leading to the recruitment and modulation of other immune cells and inflammatory factors, and inducing an uncontrolled local inflammatory response in the lungs, in a crucial mechanism underlying acute lung injury [21, 22].

Macrophages exhibit remarkable plasticity and are commonly categorized into two distinct subpopulations, characterized by the classical activation phenotype (M1) and the alternative activation phenotype (M2), which maintain a balanced state under physiological conditions but become imbalanced during disease progression [23, 24]. M1 macrophages possess proinflammatory characteristics with robust phagocytic and cytotoxic capabilities, and express proinflammatory cytokines and chemokines, such as interleukin (IL)-6, IL-12, IL-1β, TNF-α, chemokine CC ligand (CCL)2, and CCL5 [25, 26]. Conversely, M2 macrophages display an anti-inflammatory profile while playing a crucial role in tissue repair [27, 28]. Due to variations in phenotypic markers, gene expression profiles, cytokine profiles, and functional activities, M2 macrophages subtypes can be further classified into M2a, M2b, M2c, and M2d [29]. At the proteome level, M2a macrophages share similarities with M2b and M2c macrophages resemble M2d. Functionally, M2a, M2b, and M2c macrophages are primarily involved in anti-inflammatory functions, while the M2d subtype is associated with cancer development [30].

AM play a critical role in orchestrating the immune response to infections and in contributing to the pathogenesis of ARDS. Their phenotypic characteristics and functional responses show marked variability depending on the nature of the infection (viral, Gram-negative bacterial, or Gram-positive bacterial) and the inflammatory status of ARDS (hyper-inflammatory vs. hypo-inflammatory). An experimental study in mice infected with influenza A virus has demonstrated that influenza A virus (IAV) elicits significant upregulation of IL-6, granulocyte-macrophage colony stimulating factor, IFN-α, IFN-β, and IFN-γ, while exerting no discernible effects on IL-4 and IL-10. This finding suggests that M1 macrophages predominate during IAV infection [31]. A separate study involving respiratory syncytial virus-induced ALI has demonstrated that respiratory syncytial virus leads to increased levels of inducible nitric oxide synthase (iNOS), IL-6, TNF-α, and IL-4 in bronchoalveolar lavage fluid (BALF), thus significantly augmenting M1 macrophages and decreasing the proportion of M2 macrophages [32]. In cecal ligation puncture-induced ALI, significant upregulation of M1 macrophages has been observed [33]. In ALI induced by the gram-negative bacterial component lipopolysaccharide (LPS), levels of pro-inflammatory cytokines significantly increase, thus indicating a propensity for AM to polarize towards the M1 phenotype [34, 35, 36]. In the setting of acute pulmonary inflammation induced by lipoteichoic acid, a component of gram-positive bacterial cell walls, a pronounced increase in the activation and proliferation of AM has been observed [37].

Two distinct subtypes of ARDS, characterized by differential expression levels of biomarkers, have been delineated: hypo-inflammatory and hyper-inflammatory [38]. The expression levels of surface markers associated with M1 macrophages, including IL-6, IL-8, soluble tumor necrosis factor receptor 1, and IFN-γ, have been found to be significantly elevated in the high inflammation subtype compared with the low inflammation subtype [38, 39]. Moreover, a higher mortality rate has been observed in the high inflammation subtype, thus indicating distinct phenotypes of ARDS characterized by these biomarkers. In the high inflammation ARDS phenotype, M1 macrophages dominate the alveolar macrophage population. Examination of postmortem samples from patients with severe acute respiratory syndrome has revealed a predominance of macrophages, most of which are CD68-positive, in the lungs [40, 41]. In studies in patients with coronavirus disease 2019 (COVID-19), IL-6, IL-8, and IFN-γ have shown significant elevation, thereby indicating that in ARDS with a pronounced inflammatory phenotype, macrophages may adopt the M1 phenotype [42, 43, 44]. A randomized controlled trial in 115 patients with ARDS has indicated that individuals with high inflammation levels exhibit significantly higher concentrations of IL-6, IL-8, and TNF-α in their bronchoalveolar lavage fluid than those with low levels of inflammation [41, 45].

In recent years, several novel subtypes of macrophages have been identified, which secrete chemokines, metallothionein, IFN-inducible genes, and cholesterol-biosynthesis-related genes. These factors play pivotal roles in the pathogenesis and progression of ALI/ARDS. Investigation of the functional heterogeneity, activation status, and biological implications of distinct macrophage subtypes in driving inflammation, orchestrating tissue repair processes, regulating fibrosis progression, and facilitating resolution of inflammation is crucial for elucidating the pathogenesis of ALI/ARDS.

Currently, alongside the two primary macrophage subpopulations of M1/M2, lung tissue has also been found to contain CD169+, secreted phosphoprotein 1 (SPP1), and CD163+ macrophages involved in immune tolerance and antigen presentation [46, 47, 48]. Advances in experimental techniques such as single-cell RNA sequencing (scRNA-seq), high-content screening, proteomics, single-cell multiomics analysis, and fate mapping have identified novel alveolar macrophage subtypes. This discovery offers a fresh perspective for investigating the role of alveolar macrophage subtypes in preventing and treating ALI/ARDS (Table 1, Ref. [30, 34, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]).

Table 1. New subtypes of macrophages.
Species and sources of samples Cell type Biomarkers References
Bronchoalveolar lavage fluid (BALF) from patients with coronavirus disease 2019 (COVID-19) Siglec1 (CD169+) macrophages CD169+ [49]
Single-cell suspensions of macrophages derived from murine and human lung tissues Neuron and airway-associated (NAM) macrophages CD169, CX3C chemokine receptor 1, EGF-like module-containing mucin-like hormone receptor-like 1 (F4/80), Mer receptor tyrosine kinase (MerTK), CD64, high expression bone morphogenetic protein 2, CD206 (human) [50]
Patients in the advanced stage of COVID-19 SPP1 alveolar macrophages SPP1, Interleukin-1 receptor antagonist, MMP9, CHI3L1, and Platelet-Activating Factor Acetyl hydrolase [51, 52]
BALF from patients with ARDS High expression of CD169 and PD-L1 in alveolar macrophages CD169 and PD-L1 [53]
BALF from patients with ARDS AM expressing CD33, CD71, and CD163 CD33, CD71, and CD163 [53]
BALF from patients with COVID-19 Metallothionein (MT1G+) macrophages Expresses multiple thioproteins [54]
BALF from patients with COVID-19 IL-1β AM IL-1β, CCL3, and CCL4 [30]
BALF from healthy volunteers Macrophage Inflammatory Protein 1 (MIP-1) AM High expression of CCL3, CCL4, and C-X-C chemokine ligand (CXCL) 10 [55]
BALF from patients with COVID-19 Monocyte-derived AM (Mo-AM) CCL3L1 and FCGR3B [56]
BALF from patients with acute hypoxic respiratory failure (AHRF) CD163/LGMN AM High expression of CD163, legumain (LGMN), heme oxygenase 1, and Cathepsin L, and low expression of CD71 [57, 58]
BALF from healthy patients receiving LPS nebulization CD14CD16++-monocyte like cells CCL2, CCL3, CCL4, CXCL10, and CXCL11 [59]
BALF from healthy volunteers Resident AM defined by pro-inflammatory and metallothionein enzymes High expression of metal transport protein (SLC30A1) [34]

ARDS, acute respiratory distress syndrome; SPP1, secreted phosphoprotein 1; AM, alveolar macrophages; MMP9, Matrix Metallopeptidase 9; CHI3L1, Chitinase 3 Like 1; PLA2G7, Phospholipase A2 Group VII; IL, interleukin, CCL, chemokine CC ligand; EGF, epithelial growth factor; CX3C chemokine receptor 1, C-X3-C motif chemokine receptor 1; PD-L1, programmed death-ligand 1; FCGR3B, Fc gamma receptor IIIb.

Pulmonary fibrosis represents the failure of end-stage repair in ALI/ARDS. Research on COVID-19-associated fibrotic changes in this stage has identified a novel pro-fibrotic macrophage subset of AM with elevated expression of SPP1, lipoprotein lipase, and chitinase 1. These molecules contribute to the progression of pulmonary fibrosis and therefore may be potential therapeutic targets for the disease [60]. Furthermore, in vivo study using lipopolysaccharide (LPS)-stimulated ALI mice have demonstrated a significant increase in both the number and proportion of AM expressing high levels of Ly6C and CD38 in the alveoli on day 3 after LPS stimulation. Additionally, a substantial elevation was observed in the levels of iNOS, as well as the chemokines CCL2, CCL3, CCL4, CCL5, CXC motif chemokine ligand (CXCL)2, CXCL3, CXCL9, and CXCL10. After mesenchymal stem cell immunotherapy intervention, a notable decrease in the Ly6C+CD38+ macrophage population has been reported. Analysis of phenotypic and functional alterations during disease progression among macrophages has provided new insights into targeting ALI/ARDS through modulation of macrophage responses [61].

3. Methods for Analyzing Macrophage Subtypes

Many studies have demonstrated the diverse biological effects of macrophages in regulating the inflammatory response and repair processes in ALI/ARDS, with different roles in different states, indicating their pivotal role in mediating inflammation and repair [8, 62, 63]. Novel macrophage subtypes and differentially expressed genes have been identified by bioinformatics analysis of samples from healthy control and ARDS model groups, enabling exploration of the pathogenic roles of these genes and macrophage subtypes in ARDS. This knowledge could contribute to improved diagnosis, prognostic assessment, and development of novel therapeutic strategies for ARDS.

Various methods are used to investigate the functions and phenotypic analysis of macrophages (Table 2, Ref. [16, 53, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80]), primarily involving assessment of cytokine secretion and characterization of different phenotypes. In vitro experiments have used diverse features to characterize the phenotype of macrophages. For instance, M1 and M2 macrophages can be distinguished based on distinct patterns of surface receptor expression, secretion profiles, and functional characteristics [15, 81, 82]. LPS and IFN-γ are commonly used to induce M1 polarization, while IL-4 and IL-13 are utilized to induce M2 polarization. Subsequently, alterations in expression at both mRNA and protein levels can be evaluated [83, 84].

Table 2. Experimental techniques for analysis of macrophage subtypes.
Method Advantages Disadvantages References
ELISA The method exhibits high sensitivity and specificity, enabling the detection and quantification of a given marker. Poor reproducibility; many interfering factors [74, 75]
RT-qPCR The data are reliable. Absolute quantification of DNA or RNA. Long times required to design probes or primers [64, 76, 77]
Immunofluorescence This highly specific and sensitive method enables direct visualization of the nucleus and simultaneous multi-color staining. Substantial observer subjectivity [78, 79]
Flow cytometry and immunomagnetic cell sorting This method detects immune cell-related phenotypic markers; cell viability detection; cell function. High technology costs [53, 65]
HCS This method can simultaneously detect multiple candidate compounds and reveal the disease mechanisms. Experimental conditions requiring high standards [66, 67]
Proteomics This method has a high sequence coverage rate for the analysis of protein profiling. High technology costs [68, 69]
scRNA-seq This method has high resolution for construction of cell atlases, refinement of cell subpopulations, identification and analysis of rare cell types. High technology costs [70, 71]
CITE-seq This multi-omics analysis can assess the heterogeneity of immune cells. High sequencing costs; errors; limited protein markers [72, 80]
Spatial transcriptomics This method integrates multi-dimensional data and invest alterations in gene expression across various tissues. Data processing complexity [16, 73]

ELISA, enzyme-linked immunosorbent assay; RT-qPCR, real-time quantitative PCR; HCS, high-content screening; scRNA-seq, single-cell RNA sequencing; CITE-seq, sequencing.

3.1 Traditional Experimental Techniques
3.1.1 ELISA, Real-Time Quantitative PCR, and Luminex Multi-Factor Detection

Enzyme-linked immunosorbent assay (ELISA) and real-time quantitative PCR (RT-qPCR) are commonly used for assessing the polarization phenotype of macrophages, and measuring mRNA and protein levels of inflammatory factors secreted by cells during phenotypic changes [64, 85, 86]. ELISA offers the advantage of convenience and speed in detecting cell proteins, while RT-qPCR exhibits higher sensitivity and requires less cellular volume[85] . Similar to ELISA, Luminex multifactor detection enables simultaneous measurement of multiple cytokines with high sensitivity, parallel detection, and rapidity [87, 88]. ELISA and RT-qPCR are frequently utilized to determine the levels of TNF-α, IL-6, IL-1β, IL-10, iNOS, and arginase-1 in BALF and supernatants from mouse macrophage cell lines [89, 90].

3.1.2 Immunofluorescence

Immunofluorescence is an important technique that enables the visualization of diverse antigens in tissues or cell types by utilizing fluorescently labeled specific antibodies, thereby achieving exceptional sensitivity and signal amplification [91, 92]. Immunofluorescence has been used extensively in the analysis of macrophage polarization. F4/80 is commonly utilized as a marker for mouse macrophages; CD80, CD86, CD163, and iNOS are used to label M1 macrophages; and CD206, CD209, and IL-10 are used to identify M2 macrophages [93].

3.1.3 Flow Cytometry and Immunomagnetic Cell Sorting

Morrell et al. [53] used flow cytometry to discriminate between different subtypes of macrophages in BALF from patients with ARDS, and characterized immune cells in human BALF and lung tissue to distinguish surface marker profiles that differentiate alveolar from interstitial macrophages. Expression of CD169 differed significantly between human alveolar and interstitial macrophages: AM had high expression of markers such as CD169, CD71, CD80, CD86, and CD206; whereas CD169 macrophages were specifically confined to the interstitial space [65].

3.2 Analysis of Macrophages Using New Experimental Techniques

AM play a pivotal role in the pathogenesis of ALI/ARDS. Current methods for classifying macrophages primarily rely on surface marker expression and functional alterations following exogenous stimulation [83]. However, the heterogeneity of AM makes it difficult to use traditional approaches to detect the intricate internal expression changes that occur during tissue injury. Recent advances in quantitative techniques have gradually unraveled the types, states, and heterogeneity of lung macrophages.

3.2.1 High Content Screening

High-content screening (HCS) is a microscopy-based approach that enables high-throughput analysis of complex cellular phenotypes within tissue sections, while preserving cellular structure and functional integrity [66]. In comparison to conventional techniques, HCS offers improved assessment of macrophage phenotypes in diverse cell models, facilitating generation of comprehensive cellular response profiles and enabling drug discovery for disease treatment [93]. Hoffman et al. [67] employed ex vivo high-content image analysis to investigate the responses of AM to various safety medicines upon inhalation. Nizami et al. [94] have identified several small molecule inhibitors targeting heat shock protein 90, Janus kinase (JAK), and IκB kinase that effectively suppress inflammatory responses by inhibiting Nod-like receptor pyrin domain-containing protein 3-dependent apoptosis-associated speck-like protein, thereby demonstrating significant potential for predicting drug-induced macrophage polarization using in vitro safety screening tools.

3.2.2 Proteomics Technology

Significant advances in quantitative techniques have made it possible to identify thousands of proteins in a single sample. The continuous improvement of high-throughput proteomics and deep proteomic coverage further enhances our ability to validate the functional relevance of sequence variations or new transcripts identified in RNA-seq data [68]. Proteomics has emerged as a powerful tool for the diagnosis, treatment, and prognosis of diseases, and several studies have used proteomics to identify potential therapeutic targets [69, 95]. Proteomics is particularly advantageous for investigating the polarization of AM due to their high heterogeneity and the dynamic changes in cell damage during ALI [95]. Proteomic analysis characterizes the surface markers of fully polarized macrophages and elucidates the temporal alterations in cell signaling and metabolism throughout the macrophage polarization process [96]. These findings provide a solid foundation for targeted macrophage therapy [97].

3.2.3 scRNA-seq

Currently, the investigation of macrophages using the aforementioned techniques primarily relies on cell-surface-specific markers and is unable to analyze unidentified cell types. scRNA-seq, however, is not constrained by previously defined markers and enables the assessment of transcriptional similarity and diversity within cell populations [98]. Gene expression profiles can be utilized to identify distinct subpopulations, discover unique surface markers, and trace lineages, thereby offering the potential for identifying novel cell subtypes [99, 100].

In immunology research, single-cell genomics analysis aids in clustering immune cells and observing their dynamic classification into subtypes. It even allows for inference of gene regulatory networks that underlie functional heterogeneity and cell-type specificity beyond what can be achieved with current immunohistochemistry and flow cytometry methods [70]. Based on RNA-seq analysis of human and mouse lung macrophages, two distinct subpopulations were identified: CD169+CD11C- neuronal macrophages and CD169+CD11C+ airway-associated macrophages [50]. These subsets differ from other macrophage subpopulations but play crucial roles in immunoregulation and homeostasis maintenance. In organs characterized by a conserved core gene profile, tissue stratification was based on common core gene expression (phosphatidylserine receptor T cell immunoglobulin and mucin domain containing 4 (TIMD4), lymphatic vessel endothelial hyaluronan receptor 1 (LYVE1), folate receptor beta (FOLR2), and chemokine receptor C-C motif chemokine receptor 2 (CCR2)). Dick et al. [71] have further classified three macrophage subpopulations: TLF+ (expressing TIMD4 and/or LYVE1 and/or FOLR2) macrophages, CCR2+ (TIMD4-LYVE1-FOLR2-) macrophages and MHC-IIhi macrophages (TIMD4-LYVE1-FOLR2-CCR2-). scRNA-seq has now provided a new starting point for identifying disease biomarkers, new cellular subsets, therapeutic targets, and diagnostic approaches [101].

3.2.4 Cellular Indexing of Transcriptomes and Epitopes by Sequencing

While scRNA-seq enables the identification of novel cell subtypes, distinguishing functionally distinct immune cells with similar transcriptomic profiles, such as M2 macrophages across different subtypes, remains challenging. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) is an advanced technique that allows for simultaneous detection of multiomics data within individual cells [102], encompassing single-cell genomics, epigenetics, transcriptomics, proteomics, and metabolomics [103, 104]. Additionally, it facilitates quantification of cell surface protein and transcriptomic data during single-cell sequencing. By jointly analyzing proteomic and transcriptomic data sets, the gene expression profile of macrophages can be determined. Through comparative analysis of proteomics and transcriptomics in 12 distinct mouse tissue macrophages, specific molecules including Mucin 1, macrophage receptor with collagenous structure, programmed cell death ligand 1, and C-type lectin domain family 5 member A were identified to differentiate resident macrophages in tissues from lung and liver macrophages [105]. CITE-seq revealed a panel of simple cell surface protein markers (CD14, CD44, CD48, CD71, CD86, CD123 and CD163) that offer potential avenues for future research focused on identifying and purifying alveolar monocyte/macrophage subpopulations from large clinical cohorts [57].

CITE-seq enables the identification of distinct alveolar monocyte/macrophage subpopulations in patients with acute hypoxemic respiratory failure (AHRF) and facilitates the discovery of cell surface protein markers that can distinguish these subpopulations. High-throughput flow cytometry methods have been used to validate a subset of these subpopulations in an independent clinical cohort, thus revealing a significant association between CD163/legumain (LGMN) macrophages and mortality. Analysis of paired blood and alveolar samples has demonstrated that ficolin-M alveolar monocytes, inflammatory alveolar monocytes, and IFN-related macrophages exhibit transcriptomic similarities with blood monocytes [57, 58]. IL-18 has been identified as a key molecule for discriminating tissue-resident from recruited macrophages [105]. By using epigenetic sequencing and RNA-seq multiomics analysis, we identified IFN regulatory factor 1 and early growth response factor 1 as the predominant DNA-binding transcription factors expressed during M1 and M2 macrophage polarization [106]. Guilliams et al. [72] have used single-cell CITE-seq, spatial transcriptomics, and spatial proteomics datasets to establish a comprehensive spatial proteogenomic single-cell atlas of the liver while validating various surface markers for distinguishing and localizing liver macrophages. The integration of multiomics techniques is increasingly being used to assess macrophage heterogeneity while providing novel insights into diagnostic and prognostic assessment of ALI/ARDS.

3.2.5 Spatial Transcriptomics

Polarized macrophages are critical components of the innate immune response and are essential for the upkeep of lung environmental homeostasis. Nevertheless, because of the overlap in cell surface markers among tissue-resident alveolar and interstitial cells and elicited macrophages, their differentiation via conventional methodologies presents a considerable challenge. Spatial transcriptomics has substantially contributed to the delineation of macrophage heterogeneity within the lung microenvironment. By the analysis of clinical specimens derived from 646 people with COVID-19, this technique has been instrumental in differentiating ARDS and the transcriptomic alterations induced by COVID-19 from those caused by seasonal influenza viruses and other etiologies. This advancement has facilitated deeper understanding of the molecular underpinnings of COVID-19 [73]. Aegerter et al. [16] have used RNA-seq and spatial transcriptomics to proficiently delineate and differentiate human from mouse lung macrophage subsets, thereby shedding light on the maturation and functional aspects of these cells.

The analysis of macrophage subtype technology plays an essential role in the diagnosis, treatment, and prognostication of ALI/ARDS. scRNA-seq and flow cytometry can be applied to assess the proportion and activation status of distinct macrophage subpopulations during the early phases of ALI/ARDS, thereby facilitating timely diagnosis of these conditions [73]. The surface markers and secreted factors, including IL-1β, TNF-α, IL-6, and IL-18, which are pro-inflammatory mediators, detected with ELISA and qPCR in macrophages, are currently used for early diagnosis and monitoring of ALI/ARDS [107]. These biomarkers also serve as crucial indicators for evaluating the severity and prognosis of ALI/ARDS [108]. CITE-seq in in patients with AHRF has revealed that CD163/LGMN macrophages are a distinct set of macrophage subpopulations associated with mortality [57]. Moreover, these methods for characterizing macrophage subpopulations can also facilitate the development of individualized therapeutic strategies. On the basis of the diverse phenotypes of macrophages, HCS offers technical support for in vitro drug safety prediction [94]. The identification of specific signaling pathways in different macrophage subtypes through single-cell sequencing, CITE-seq, and spatial transcriptomics provides novel targets for precision therapy. As research advances, analysis of macrophage subtypes will further advance clinical management and optimize treatment strategies for ALI/ARDS.

4. Application of Macrophage Subtype Analysis in the Study of ALI/ARDS
4.1 Application in Different Stages of ALI

The duration, degree, and proportion of macrophage polarization, as well as the subpopulation of macrophages, play crucial roles in determining the severity and prognosis of ALI/ARDS [109]. During the exudative phase of ALI/ARDS, M1 macrophages are predominantly activated by pathogens, leading to elevated levels of IL-1β and TNF-α in plasma and BALF. Additionally, proinflammatory cytokines IL-6 and IL-8 are significantly increased in plasma and BALF, serving as potential predictors of poor outcome [108, 110, 111]. The recent study conducted on mice with ALI/ARDS revealed a significant increase in the number and proportion of highly expressed Ly6C and CD38 macrophages in BALF on day 3. This was accompanied by an increase in proinflammatory cytokines iNOS, IL-6, and IL-1β, as well as chemokines [61]. A single-center cohort study focusing on COVID-19 patients indicated a significant increase in the number of inflammatory IL-1β AM, along with higher expression levels of inflammatory factors and chemokines observed in severe cases. However, these macrophages returned to normal numbers and function during recovery [112]. In a trial aimed at preventing ARDS in high-risk patients in emergency departments, the assessment of inflammatory subphenotypes of ARDS included IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, and TNF-α as crucial criteria [113].

M2 is the predominant macrophage subtype involved in the resolution phase of ALI/ARDS, and plays a pivotal role in regulating excessive inflammatory responses and promoting anti-inflammatory and wound healing processes. M2a and M2c macrophages possess the ability to modulate Janus kinase (JAK) signal transducer and activator of transcription (JAK-STAT) pathway activation through IL-10 in LPS-induced ALI, thereby mitigating inflammatory infiltration and preserving lung function in murine models [114].

Many studies have demonstrated that the fibrotic phase of ALI/ARDS primarily correlates with M2 macrophages expressing diverse cytokines, including CD206 and chemokine CCL18. The levels of cytokines IL-10 and transforming growth factor-β (TGF-β) are commonly regarded as indicators for lung tissue fibrosis progression, with TGF-β promoting myofibroblast proliferation and extracellular matrix deposition. IL-10 produced by neutrophils in the lungs induces polarization towards M2c macrophages, which subsequently secrete TGF-β to facilitate fibrosis [114, 115]. Apart from M2 macrophages, novel subtypes of macrophages associated with pulmonary fibrosis have also been identified. In mouse models of pulmonary fibrosis, a subset of AM expressing SPP1, chitinase 3 like 1 (CHI3L1), myristoylated alanine-rich C-kinase substrate, interleukin-I receptor antagonist, phospholipase A2 group VII (PLA2G7), and matrix metallopeptidase 9 (MMP9) has been characterized. The recent study has highlighted SPP1 and CHI3L1 as key promoters of pulmonary fibrosis. SPP1 disrupts the balance between M1/M2 macrophages by inhibiting von Hippel-Lindau tumor suppressor expression and hypoxia inducible factor 1α degradation, thereby exacerbating ALI/ARDS [116]. Elevated levels of surface markers CD163, SPP1, and CCL18 were observed in BALF samples from COVID-19 patients with severe late-stage ALI, indicating progression towards pulmonary fibrosis during advanced stages of ALI/ARDS [48]. With advances in experimental techniques, newly identified subtypes of AM offer novel avenues for predicting disease severity and prognosis (Fig. 1).

Fig. 1.

Dynamic changes in macrophages during the inflammatory, recovery, and fibrotic phases of ALI/ARDS. Upon viral infection, AM recognize pathogen-associated molecular patterns and undergo polarization into M1 phenotype, leading to the release of proinflammatory cytokines that contribute to tissue damage. Novel macrophage subsets, such as Ly6C+CD38+ and CD169+ macrophages, also participate in the response to tissue injury. In later stages of damage, AM transition from the M1 to the M2 phenotype and secrete anti-inflammatory cytokines that facilitate tissue repair. Notably, SPP1-expressing macrophages and CD163/LGMN-positive macrophages significantly increase during the fibrotic phase of ALI/ARDS and play a pivotal role. ALI, acute lung injury; M0, nonactivated phenotype; M1, classical activation phenotype; M2, alternative activation phenotype; TNF, tumor necrosis factor; TGF, transforming growth factor-β; VEGF, Vascular endothelial growth factor; iNOS, inducible nitric oxide synthase; Ly6C, lymphocyte antigen 6 family member C1; ARDS, acute respiratory distress syndrome. The figure was created by Figdraw (https://www.figdraw.com).

4.2 Application of Macrophage Subtype Analysis in the Selection of Treatment Strategies for ALI

By investigating novel subtypes of macrophages and identifying appropriate targets, it may be feasible to slow disease progression and enhance patient survival rates. Tailored therapeutic strategies can be developed for distinct macrophage subtypes. Numerous targeted therapeutic approaches for macrophages have been developed to modulate macrophages from a proinflammatory to an anti-inflammatory state, enhance the anti-inflammatory phenotype of macrophages, suppress the proinflammatory phenotype, and target signaling pathways associated with inflammation. These strategies encompass pharmaceutical agents, nanoparticles, small interfering RNA, and cell-based therapy specifically designed for targeting macrophages (Fig. 2) [117, 118, 119, 120, 121, 122].

Fig. 2.

Diagram depicting diagnosis and treatment of ALI. (A) Identification of novel subtypes of macrophages in blood and BALF, based on their specific surface markers and proportions, holds promise for prognostic assessment of disease outcome. (B) Various cellular tools can be reprogrammed into macrophages. (C) Therapeutic strategies targeting inhibition of macrophage proinflammatory activity and promotion of anti-inflammatory responses involve the use of drugs, nanoparticles, and exosomes for ALI management (Fig. 2). EVs, extracellular vesicles. The figure was created by Figdraw (https://www.figdraw.com).

4.2.1 Medicine

Despite extensive research on ALI/ARDS, the current optimal clinical approach for ALI/ARDS remains protective mechanical ventilation; however, the mortality rate has not declined. Investigating alternative molecular mechanisms beyond supportive therapy is imperative to decrease mortality. For instance, inhibiting the amplification of signaling pathways may provide an efficacious strategy for managing ALI [123, 124]. If emodin reduces the production of exosomes from isocitrate dehydrogenase 1 pancreatic acinar cells, it weakens the polarization of macrophages towards M1 type macrophages by inhibiting the peroxisome proliferator-activated receptors γ (PPARγ)/nuclear factor-kappaB (NF-κB) pathway, thus alleviating severe acute pancreatitis-associated acute lung injury [125]. Exosomal miR-30d-5p from neutrophils targets cellular signaling inhibitor 1 and sirtuin 1 to activate NF-κB signal transduction, induce M1 polarization of macrophages, and trigger macrophage pyroptosis [126]. In a study of severe COVID-19 patients, a new subtype of AM expressing high levels of Fc gamma receptor IIIb (FCGR3B) and C-C motif chemokine ligand 3 like 1 (CCL3L1) was identified, and kyoto encyclopedia of genes and genomes and gene ontology enrichment analyses clarified that the newly identified macrophages participated in TNF-α-related host immune responses and cytokine and IFN-γ responses. This suggests that the identified macrophage subtype or the FCGR3B gene may aggravate severe COVID-19 [56]. In another study of LPS-ALI mice, mesenchymal stem cells significantly downregulated the number of proinflammatory macrophages expressing high levels of Ly6C and CD38 and chemokines [61]. In mice with LPS-ALI, grape seed proanthocyanidins regulated the triggering receptor expressed on myeloid cells/phosphatidylinositol 3-kinase/protein kinase B pathway to modulate M2a macrophage polarization, thereby ameliorating the development of ALI [127]. In another study, M2a and M2c macrophages regulated the activation of the JAK/STAT signaling pathway by IL-10 to alleviate inflammation and lung function damage in LPS-ALI mice. The authors also found that M2c macrophages were more effective than M2a macrophages in preventing lung damage and fibrosis [114]. Nuclear factor erythroid-derived 2-like 2 regulates macrophage polarization from M1 to M2 to alleviate ALI via autophagy and the NF-κB/PPARγ pathway [128].

4.2.2 Nanomedicine

Nanocarriers hold substantial promise for overcoming the limitations of conventional drug therapy for ALI/ARDS by facilitating targeted delivery to specific cells, precise drug release, and improved pharmacokinetics and pharmacodynamics [129, 130]. Su et al. [131] have prepared dexamethasone (DXM)/mannose co-modified branched polyethyleneimine (DXM-PEI-mannose, DPM) prodrug nanoparticles that effectively target the mannose receptor on AM in the lungs, thus offering a potential treatment for ALI/ARDS. DXM-PEI exhibits excellent serum stability and biocompatibility. Furthermore, DXM-PEI significantly decreases the infiltration of inflammatory cells and TNF-α content in mouse lung tissue, thereby ameliorating ALI/ARDS. Gao et al. [132] have prepared phenylboronic acid-functionalized generation 5 poly(amidoamine) dendrimers loaded with fibronectin, which downregulate TNF-α, IL-1β, and reactive oxygen species levels, and promote the polarization of macrophages towards the M2 phenotype, thus providing a potential therapeutic approach for ALI.

Gene silencing is a promising paradigm for specifically and effectively inhibiting these mechanisms, thereby creating new treatment opportunities for ALI/ARDS. The modulation of pro-inflammatory mediators at the mRNA level in ALI/ARDS can be achieved through short interfering RNA (siRNA), thereby demonstrating the potential of gene silencing as an effective molecular therapy for treating lung injury by targeting siRNA to lung tissue. Intrabronchial administration of siRNA significantly attenuates the production of pro-inflammatory cytokines in the lungs by suppressing NF-κB activity, thus ameliorating acute lung injury induced by cigarette smoke. Receptor-interacting protein 2 is therefore a promising therapeutic target for the treatment of ALI [133]. M2-Exos mitigate pulmonary injury and inflammation by transporting miR-370, which in turn suppresses the FGF1/MAPK/STAT1 axis and retards the progression of asthma [134]. Nevertheless, the utility of free siRNA is constrained by its substantial molecular weight, abundant negative charge, and limited stability [124, 135]. Innovative nanoparticles can facilitate siRNA transfection in vitro [135]. Weng et al. [136] have conducted a nanoscale Zr(IV)-based porphyrin metal-organic framework to deliver small interfering zinc finger E-box binding homeobox 1 and 2, thus mitigating early fibrotic changes after ALI. In vivo experiments have demonstrated the ability of this Zr(IV)-based porphyrin metal-organic framework to selectively target inflamed lung tissue in animal models. Pyrrolidinium-modified amphiphilic generation 1 phosphorus dendron nanomicelles can be sued to co-deliver the miRNA-146a mimic and miRNA-429 inhibitor, and consequently suppress the polarization of M1 AM and mitigate ALI [137]. Furthermore, the integration of Clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated nuclease 9 (Cas9) gene editing with an inhalation delivery system holds promise for mitigating ALI. Huang et al. [138] have proposed a strategy combining CRISPR/CRISPR-associated nuclease 9 gene editing with an inhalation delivery system to encapsulate a core-shell liposomal nanoplatform for precise HK2 downregulation, targeting pulmonary macrophages, and decreasing macrophage glycolysis and inflammation, thereby offering a potential treatment for ALI.

4.2.3 Cell-Based Therapy

Recent studies have proposed that targeted cell-based therapy specifically aimed at macrophages could be a promising therapeutic strategy for ALI/ARDS [139, 140, 141]. This can be achieved by introducing multipotent/hematopoietic stem cells into the trachea via intubation, followed by in vivo induction of their differentiation into macrophages. These differentiated macrophages can then mitigate the progression of ALI/ARDS through neutrophil phagocytosis and promotion of lung tissue repair. A multi-center study in patients with COVID-19 has demonstrated that transplantation of mesenchymal stem cells significantly decreases the mortality rate in patients with acute lung injury/acute respiratory distress syndrome induced by epidemic influenza A (H7N9) infection [142, 143]. Additionally, in vitro induction of an anti-inflammatory and repair-promoting state in macrophages, followed by injection of healthy macrophages into the lungs, can rectify immune dysregulation and suppress cytokine storms, thereby enhancing the survival rate of patients with ALI/ARDS [144]. Gorki et al. [121] showed that primary AM were successfully transplanted into mice with alveolar macrophage deficiency. This transplantation effectively decreased the accumulation of surfactants and proteins in the lungs of mice lacking pulmonary AM, thus demonstrating their ability to perform crucial macrophage functions when implanted in vivo. Another study has indicated that repeated stimulation of alveolar macrophage subpopulations with LPS or Pseudomonas aeruginosa expressing high levels of MERTK and macrophage receptor with collagenous structure, and low levels of CD163 and F4/80+, accelerates the resolution of lung injury and decreases mortality in mice with Pseudomonas aeruginosa-induced acute lung injury after transfer of these cells into the lungs [145]. Furthermore, Aegerter et al. [146] have demonstrated that mice that have recovered from COVID-19 for 1 month are protected against Streptococcus pneumoniae infection, a finding potentially attributed to the presence of IL-6-high AM derived from monocytes in the lungs. A separate study has revealed that the subtype of pulmonary macrophages in mice experiencing recurrent pneumococcal infections differs from that of resident alveolar macrophages, and that a novel subtype suppresses bacterial proliferation during repeated infection [147] .

Consequently, maintaining a balanced inflammatory state within macrophages and targeting them specifically may represent a pivotal therapeutic approach for ALI/ARDS.

4.3 Analysis of Macrophage Subtypes for the Assessment of Prognosis in ALI

Previous studies have demonstrated that the analysis of macrophage subtypes in ALI/ARDS through the utilization of cell surface markers and gene expression profiling has potential for prognostic assessment of disease progression. In a single-center study, multivariate analysis of patients with ALI/ARDS demonstrated direct correlation between the level of IL-8 in BALF and patient mortality [107, 108, 148]. Proinflammatory cytokines such as IL-1β, TNF-α, IL-6, and other inflammatory factors produced by M1 AM, have been identified as potential predictors of adverse clinical outcomes [107]. A clinical study in patients with COVID-19 has indicated that the expression of interferon response genes in BALF is directly associated with prognosis. Recovered patients exhibited reduce expression of interferon response genes, whereas no change in interferon response gene expression was observed in deceased patients [148]. Novel techniques to identify new subtypes of AM can also aid in assessing disease severity and prognosis. Morrell et al. [57] used CITE-seq to discover high CD163 and low CD71 cell-surface protein expressed on CD163/LGMN AM along with a mature macrophage subpopulation characterized by high expression of CD163 and CD71. They found that the proportions of these subpopulations were not only associated with fibrosis in patients with AHRF, but also correlated with mortality rates. Fan and colleagues have identified a substantial presence of CXCL10+CCL2+ macrophages in the BALF in severely ill patients with COVID-19, thus suggesting that this population may represent a potential target for existing immunotherapies [149]. Additionally, an analysis of clinical samples from COVID-19 patients revealed significant upregulation of genes in monocyte macrophages, which demonstrated the potential for predicting severity of COVID-19 [57, 58].

Distinct cell subpopulations and cytokines have been identified in ALI/ARDS patients with a favorable prognosis. One study reported elevated levels of granulocyte–macrophage colony-stimulating factor in BALF among patients with improved prognosis for ARDS [150]. A single-center trial observed a reduction to baseline levels in the number and proportion of IL-1β-producing macrophages in BALF during the recovery phase of severe COVID-19. Therefore, subtype analysis offers a novel approach for assessing the severity and prognostic implications of ALI/ARDS [57].

5. Conclusion and Outlook

Macrophages are the most abundant immune cells in alveoli and play crucial roles in regulating inflammation and promoting tissue repair during ALI/ARDS [10]. Macrophages can differentiate into various subtypes due to their high heterogeneity in different environments [151]. Advanced experimental techniques such as scRNA-seq, proteomics analysis, single-cell multiomics analysis, fate maps, and bioinformatics analysis have gradually revealed new macrophage subtypes with distinct secreted inflammatory factors, surface-specific markers, and epigenetic profiles.

Conventional experimental techniques continue to be widely used for evaluation of diverse functions and phenotypes of macrophages. Approaches such as scRNA-seq, proteomics analysis, and single-cell multiomics analysis are indispensable in constructing immune cell atlases, refining cellular subpopulations, and identifying rare cell types. Despite recent advances, these methods still have limitations, including high technical costs and limited coverage at the single-cell level, necessitating further enhancements and exploration.

ALI/ARDS has long been recognized as a highly heterogeneous clinical syndrome due to the diverse array of pathogenic factors, clinical symptoms, onset time, and disease course [3]. In healthy or diseased states, different subsets of macrophages have specific locations and functions. In the early stage of ALI/ARDS, M1 macrophages predominate in the alveoli, and play a proinflammatory and pathogen-clearing role. In the late stage of the disease, M2 macrophages secrete large amounts of inflammatory factors to promote tissue remodeling and repair [25]. In addition, during the progression of ALI/ARDS, the numbers and proportions of new subpopulations of CD163/LGMN AM, Ly6C+CD38+ AM, and SPP1 AM are upregulated. These cells have different numbers and proportions in alveoli depending on patient age, severity of ARDS, ARDS stage, and treatment during progression, and to some extent, they can directly predict the mortality rate. Therefore, more precise phenotypic analysis is needed to study the new subpopulations of macrophages and their dynamic changes in the disease process, and to explore the relationship between these dynamic changes and clinical outcomes.

The exploration of novel subtypes of macrophages is anticipated to advance our understanding of the pathogenesis, diagnosis, and treatment of ALI/ARDS. However, the clinical significance of these newly identified macrophage phenotypes in diagnosing and assessing prognosis for ARDS remains undetermined, necessitating further investigation into the specific alterations occurring in macrophages during inflammatory and reparative processes. This will provide valuable insights for selecting diagnostic markers and identifying potential therapeutic targets.

Currently, targeted macrophage or macrophage-based therapies are still in the early stages; however, they have demonstrated promising outcomes in experimental models of ALI/ARDS [117, 119]. For instance, this includes the conversion of mesenchymal and hematopoietic stem cells into macrophages, followed by their administration via tracheal injection in mice [139]. Additionally, there is potential for drugs, nanoparticles, and exosomes to modulate macrophages from a proinflammatory to an anti-inflammatory state [122, 125, 126]. Consequently, further investigation into strategies for targeted macrophage therapy is imperative to establish a solid foundation for clinical translation.

Abbreviations

ALI, acute lung injury; ARDS, acute respiratory distress syndrome; AHRF, acute hypoxemic respiratory failure; BALF, bronchoalveolar lavage fluid; SPP1, secreted phosphoprotein 1; scRNA-seq, single-cell RNA sequencing; LPS, lipopolysaccharide; IFN, interferon; TNF, tumor necrosis factor; IL, interleukin; CCL, chemokine CC ligand; iNOS, inducible nitric oxide synthase; HCS, high-content screening; JAK, Janus kinase; TIMD4, phosphatidylserine receptor T cell immunoglobulin and mucin domain containing 4; LYVE1, lymphatic vessel endothelial hyaluronan receptor 1; FOLR2, folate receptor beta; CCR2, chemokine receptor C-C motif chemokine receptor 2; TGF-β, transforming growth factor-β; CHI3L1, Chitinase 3 Like 1; PLA2G7, Phospholipase A2 Group VII; MMP9, Matrix Metallopeptidase 9; NAM, neuron and airway-associated macrophages; FCGR3B, Fc Gamma Receptor IIIb; CCL3L1, C-C motif Chemokine Ligand 3 Like 1; AM, alveolar macrophages; IM, interstitial macrophages; TR-AM, tissue-resident alveolar macrophages; Mo-AM, monocyte-derived alveolar macrophages; IAV, influenza A virus; siRNA, short interfering RNA; DXM, dexamethasone; DPM, dexamethasone mannose co-modified branched polyethyleneimine; CD64, Fc gamma receptor I; F4/80, EGF-like module-containing mucin-like hormone receptor-like 1; MerTK, Mer receptor tyrosine kinase; Siglec F, Sialic acid binding Ig-like lectin F; LGMN, Legumain; CXCL, CXC motif chemokine ligand.

Author Contributions

JT and JS contributed equally to this work. JT and JS recommended a structure for the review and wrote the initial draft. ZH and XC revised the manuscript and prepared figures. All authors read and approved the final manuscript. All authors have participated sufficiently in the work and agreed to be accountable for all aspects of the work.

Ethics Approval and Consent to Participate

Not applicable.

Acknowledgment

We would like to express our gratitude to all the peer reviewers for their opinions and suggestions.

Funding

This research was funded by the Natural Science Foundation of Beijing Municipality (NO.7232169).

Conflict of Interest

The authors declare no conflict of interest.

References

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