scRNA-Seq of lung macrophages over time courses of LPS- and bleomycin-induced lung injury and repair. The goal of this study was to identify differences in macrophage subsets between self-limited lung injury with nonfibrotic repair and prolonged injury with dysregulated repair and fibrosis. To achieve this, we employed 2 mouse models to represent these divergent outcomes of ARDS. LPS induces acute lung injury that fully resolves without fibrosis within 2 weeks, while bleomycin induces injury that progresses to fibrosis before eventual resolution over 2 months (Supplemental Figure 1; supplemental material available online with this article; https://doi.org/10.1172/jci.insight.182700DS1).

A long-standing barrier in the field is a lack of cell surface markers that reliably distinguish resident from recruited IMs over the course of inflammation. To address this challenge, we pulsed Cx3cr1-TdTomato mice with tamoxifen to label all RIM. Since this strategy also labeled circulating monocytes, we waited for 4 weeks to allow monocytes to turn over and then administered LPS or bleomycin (38). Lungs were harvested on days 3, 6, and 15 after LPS and days 3, 7, and 14 after bleomycin (Figure 1A). These time points correspond to early neutrophilic inflammation, early repair, and late repair in both models (Supplemental Figure 1). Immediately after euthanasia, anti–mouse CD45 antibody was instilled i.t. (IT CD45) to label all immune cells in the airspaces (13). Lungs were digested, and 3 macrophage populations were simultaneously sorted: all AMs, RecIM, and RIM (Figure 1B and Supplemental Figure 2). While this sort strategy enabled lineage tracing and anatomic localization, it masked information regarding relative population sizes between sorts. To address this, we simultaneously collected a fourth set of sorted cells from each lung containing total CD45+ leukocytes. Each population was sequenced separately to preserve spatial and lineage identification.

Macrophage isolation and scRNA-Seq following bleomycin and LPS-induced lung injury. (A) Timeline of interventions in experimental models. Tamoxifen was given to label resident interstitial macrophages followed by a 4-week wait period to allow clearance of labeled monocytes from the circulation. Mice were treated with i.t. LPS (20 μg) or bleomycin (1.5 U/kg) and were euthanized at the times indicated. Anti-CD45 antibody was instilled into the lungs immediately after euthanasia. (B) Four groups of cells were isolated from digested lung tissues using FACS. These included airspace macrophages (AMs), resident IMs (RIM), recruited IMs (RecIM), and general leukocytes (CD45+). AMs versus IMs were distinguished based on i.t. administered anti-CD45 labeling. Resident versus recruited IMs were distinguished by tdTomato expression. (C) Fully integrated UMAP including all sorted cells from day 0; LPS days 3, 6, and 15; and bleomycin days 3, 7, and 14. Clusters were manually annotated based on cluster-defining genes. Macrophage clusters are outlined in the dashed black line. (D) UMAP split to show homeostasis, LPS, and bleomycin samples. (E) Feature plot of the log2 minimum expression of mouse panmacrophage markers Fcgr1, C5ar1, CD68, Mrc1, and Mertk. (F) Average expression and percent of cells expressing panmacrophage marker genes in each cluster. Macrophage clusters in the dashed black box were used in subsequent analyses.

Individual sequencing libraries were integrated into a single dataset incorporating all time points and models. From this common dataset, Seurat clustering yielded 34 distinct cell types that were manually annotated using LungMAP (39) murine marker genes (Figure 1C and Supplemental Figure 3). As anticipated, the dataset was greatly enriched for macrophage populations. Other myeloid and lymphoid cell subsets were also captured in the CD45+ sort libraries as well as small numbers of structural tissue cells, particularly endothelial cells. Splitting the Uniform Manifold Approximation and Projection (UMAP) by homeostasis versus injury models revealed that lung structural cells and tissue resident immune cells dominate at homeostasis. In lungs from LPS- and bleomycin-treated mice, additional macrophage clusters were present and other leukocyte clusters were expanded, consistent with inflammatory responses (Figure 1D). Pan-macrophage markers Fcgr1, C5ar1, Cd68, Mertk, and Mrc1 were used to identify macrophage clusters in the aggregate dataset (Figure 1, E and F). The cluster annotated as “Mito IM” was excluded from further analysis due to high enrichment for mitochondrial RNA transcripts.

Macrophage clusters are defined by origin and compartment. To enable granular analysis of macrophage subsets, clusters identified as macrophages in the global UMAP were subclustered, identifying 8 macrophage subsets (Figure 2A). Cluster 3 was removed from subsequent analysis because it lacked differentially expressed genes (DEGs) and was instead defined by overall low gene expression relative to other clusters. Proliferating cells were not included in the subclustering.

Macrophage clusters correspond to compartment and origin. (A) Macrophage-specific UMAP generated by reclustering macrophage clusters from the global UMAP. (B) Relative contribution of alveolar macrophages (AM) versus interstitial macrophages (IM) to each cluster, based on sort (AM versus IM) from which the cells were derived. (C) Feature plots of the AM sort from all time points and models showing expression of Siglecf and Itgam, and a UMAP showing the AM sorts exclusively from homeostasis samples. (D) Fraction of cells derived from RIM versus RecIM sorts for IM clusters. (E) Feature plots of IMs from all time points and models showing expression of Folr2 and Ccr2, and a UMAP showing IMs derived exclusively from homeostasis samples. (F) Dot plot of selected marker gene expression for the 7 macrophage clusters. (G) Cytoscape network visualization of GO pathways enriched in the marker lists for each cluster. Nodes correspond to individual pathways, and edges connect nodes with shared genes. Edge color indicates the cluster that is most highly enriched for that pathway; however, multiple clusters may be enriched for a given pathway. (H) DecoupleR transcription factor inference heatmap showing activity scores of the top 25 most variable transcription factors between the 7 clusters.

Because pulmonary macrophage programming is influenced by location, we first sought to assign each of the remaining 7 clusters to the airspace or interstitial compartment. Using the sort information encoded in the dataset, the proportion of cells derived from alveolar macrophage (AM) versus interstitial macrophage (IM) sorts was determined for each cluster (Figure 2B). Clusters 4 and 6 were predominately AMs. Cluster 0 was split between AMs and IMs, while clusters 1, 2, 5, and 7 were dominated by IMs.

Since macrophage programming is tightly linked to ontogeny during inflammation, we next sought to identify the origin of cells within each cluster (12). In the airspace, RAM and RecAM can be reliably distinguished by expression of Siglec-F (Siglecf) and CD11b (Itgam) (40). Accordingly, we found clusters 4 and 6 had high expression of Siglecf, suggesting that these clusters were composed of RAM. In comparison, cluster 0 exhibited high Itgam expression consistent with RecAM. To further confirm origin, we mapped cells in AM sorts from homeostasis. Homeostatic AMs overlaid clusters 4 and 6, confirming their RAM identity, while cluster 0 was nearly absent at homeostasis (Figure 2C). To identify the origin of IM clusters, we determined the proportion of resident versus recruited cells within each IM cluster using RIM and RecIM sort information. This suggested that clusters 1 and 2 were a mix of RIM and RecIM, cluster 5 was predominately composed of RecIM, and cluster 7 contained RIM (Figure 2D). To confirm these findings, we evaluated IM clusters for expression of selected genes. Since no markers exist that reliably distinguish all RIM subsets from RecIM subsets, we evaluated Folr2, which marks a subset of RIM, and Ccr2, which marks all RecIM but is also expressed by a subset of RIM (11, 13). We again used the homeostasis samples to confirm that cluster 7 is composed of RIM, cluster 5 contains RecIM, and clusters 1 and 2 have both RIM and RecIM (Figure 2E).

After identifying the contribution of compartment and origin to cell clustering, we sought to define specific marker genes for each cluster. We first identified cluster marker genes within each sample, and we next determined a conserved set of markers for each cluster that were significantly differentially expressed in at least 80% of samples. This led to identification of specific, conserved marker genes for each cluster except for clusters 4 and 6, which had overlapping markers, albeit with different expression levels (Supplemental Table 1). As a final step, we combined assessments of maker genes, compartment, and origin to assign the following identifiers to each cluster: 0 = Gpnmb RecAM, 1 = Mmp12 IM, 2 = Tmem119 IM, 4 = Ear1hi RAM, 5 = Irf7 RecIM, 6 = Ear1int RAM, and 7 = Folr2 RIM (Figure 2F). These cluster identities are similar to macrophage subsets described in previous studies (11, 13).

Using the conserved markers for each cluster, we performed gene set enrichment analysis to infer cluster-specific functions. In the Cytoscape Enrichment Map network visualization tool, individual nodes correspond to Gene Ontology (GO) pathways and edges connect nodes with overlapping gene sets (41, 42). Edges were colored according to the cluster with the lowest adjusted P value, although multiple clusters may have significant enrichment for a given pathway (Figure 2G and Supplemental Table 2). As expected, RAM cluster marker genes were enriched in fatty acid, lipid, and cholesterol metabolism pathways, highlighting their roles in lung surfactant processing. Other pathways enriched in RAM related to endocytosis and tissue development, again suggesting homeostatic functions. In comparison, Gpnmb RecAM were uniquely enriched for pathways related to redox stress, immune activation, and cellular reorganization. In the IM compartment, Folr2 RIM were enriched for pathways related to lung morphogenesis, blood vessel development, and myeloid chemotaxis and immune activation, suggesting that these cells play key homeostatic roles by maintaining lung structure and immune cell tone. Mmp12 IM were enriched for antigen processing and presentation pathways but were also enriched for cellular response pathways containing Egr1, a transcription factor shown to suppress the inflammatory response (43). Tmem119 IM shared enrichment for inflammatory response pathways with Mmp12 IM but were uniquely enriched for complement activation and creatine metabolism pathways. Lastly, Irf7 RecIM were enriched for immune-related pathways, including response to pathogens, secretory granules, and antigen processing and lymphocyte activation, suggesting a proinflammatory function.

To identify putative transcription factors that underlie distinct subset identities, we performed transcription factor inference analysis via decoupleR and calculated the top 25 most variable transcription factors between clusters (Figure 2H) (44). Ear1hi and Ear1int RAM shared 9 transcription factors and were characterized by PPAR transcription factors, which are key regulators of lipid and carbohydrate metabolism (45, 46). A key transcription factor of the Folr2 RIM was Mafb, which is known to drive antiinflammatory programming in macrophages (47). Mafb activity was also higher in Mmp12 IM and Tmem119 IM and may be a driver of monocyte-to-IM maturation (48). Irf7 RecIM had high activity of proinflammatory transcription factors downstream of type I and type III IFN signaling. Lastly, the Gpnmb RecAM had no unique high-activity transcription factors, which may reflect the low number of conserved markers (Supplemental Table 1).

Macrophage cluster sizes vary by time and injury model. Having determined the compartment and origin of each macrophage cluster, we next asked whether any clusters were unique to an injury model or time point. To eliminate proportion bias from macrophage-enrichment sorts, macrophage cluster proportions were calculated from CD45+ sorts (Figure 3A). All clusters were present at all postinjury time points in both models, indicating that Seurat clustering did not identify exclusively model- or time-specific clusters. Principal component analysis of average log-normalized expression of cells from AM, RIM, and RecIM sorts at each time point in each model confirmed that compartment and origin were the strongest determinants of clustering, followed by time point and injury model (Supplemental Figure 4).

Macrophage cluster sizes vary over time and between models. (A) Macrophage UMAP split by model and time point. Vertical bars show the percent contribution of each cluster in the CD45+ sort to the macrophage pool for each model and time point. (B) Total macrophage numbers in the lungs from mice treated with i.t. LPS or bleomycin. (C–I) Estimated cell numbers for clusters in LPS (purple) versus bleomycin (green). (J) Heatmap of cell counts for each cluster at each model time point. Line graphs in B–I show mean ± SEM.

Although none of the clusters were model specific or time specific, we observed substantial differences in cluster proportions between models and time points (Figure 3A). Since total macrophage numbers also differ between the LPS and bleomycin models over time (Figure 3B), we combined them with cluster proportions from CD45+ sorts (Figure 3A) to determine total macrophage numbers for each cluster over time. This revealed model-specific differences in population kinetics of resident and recruited macrophage clusters. In particular, Ear1hi and Ear1int RAM numbers rapidly decreased at early time points following bleomycin challenge before returning to baseline at day 14, whereas in the LPS model, they remained stable at early time points and then transiently expanded at day 6 before eventually returning to baseline (Figure 3, C and D). In contrast, RecAM and RecIM clusters exhibited rapid expansion at early time points in both models. However, in LPS-treated mice RecAM and RecIM clusters returned to baseline by day 15, whereas in bleomycin-treated mice, they remained elevated (Figure 3, E–G). Folr2 RIM numbers remained stable throughout inflammation in both models (Figure 3I). In summary, no model- or time-specific macrophage clusters were identified. Instead, model-specific differences were found by examining cluster sizes over time, with early, transient loss of RAM and later persistence of RecAM and RecIM in the bleomycin model compared with LPS (Figure 3J). Notably, numbers of recruited macrophages were remarkably similar between models during the initiation of inflammation.

Macrophages with profibrotic gene expression are found in lungs from bleomycin- and LPS-treated mice and in humans with fibrotic and nonfibrotic diseases. We initially hypothesized that our analysis would reveal a fibrosis-associated macrophage subset unique to the bleomycin model; however, we found no model-specific clusters. We therefore investigated the expression of fibrosis-associated genes in our macrophage clusters using a published list of fibrosis-associated macrophage genes validated in lung tissue from humans with pulmonary fibrosis and mice with asbestos- and bleomycin-induced fibrosis (20). We compared expression of these “fibrotic features” between the 7 macrophage clusters without separating cells from models or time points (Figure 4A). All clusters expressed genes from the list; however, comparison of the conserved cluster marker lists to the fibrotic features list demonstrated that Gpnmb RecAM were highly enriched for these fibrotic features.

Gpnmb RecAM macrophages are found in fibrotic and nonfibrotic lung disease in mice and humans. (A) Dot plot of expression of fibrosis-associated macrophage marker genes (fibrotic features) in macrophage clusters, scaled across rows. For each cluster, enrichment scores were calculated comparing the overlap of conserved cluster markers and fibrotic features to the expected number of overlapping genes by chance. These are represented in the heatmap. Data are from LPS and bleomycin models and include all time points. (B) Violin plot of fibrotic features gene set scores in Gpnmb RecAM from each model and time point. (C) Violin plot of fibrotic features gene set scores in macrophage clusters from homeostasis. (D–G) Heatmap of enrichment scores of the Gpnmb RecAM gene set and the fibrotic features gene set in macrophage subset marker lists from: human IPF lungs (D), healthy human bronchoalveolar lavage (E), human severe COVID-19 (F), allergic asthmatics and nonasthmatic controls (G), nonfibrotic murine models of pulmonary pneumocystis infection (H), and skin wounds in healthy and diabetic mice (I). Hypergeometric tests in B and C. *P < 0.05, ***P < 0.0005, *****P < 0.000005.

To determine if the expression of these fibrotic features in Gpnmb RecAM was model or timespecific, we calculated a gene score to compare the average expression of fibrotic features between Gpnmb RecAM from each time point in each model. Briefly, fibrotic features scores were calculated for each cell in the Gpnmb RecAM cluster by taking the average of the centered and scaled expression of genes in the fibrotic features gene set. Fibrotic feature scores were elevated in Gpnmb RecAM from all LPS and bleomycin inflammatory time points compared with homeostasis, except for LPS day 15 (Figure 4B). Moreover, Fibrotic Feature scores were not different between the corresponding LPS and bleomycin time points except for day 14 versus 15 (day 14/15). Notably, comparison of fibrotic feature scores for all macrophage subsets at homeostasis continued to identify Gpnmb RecAM as “fibrotic” relative to other macrophage clusters (Figure 4C). Taken as a whole, these data show that Gpnmb RecAM had greater expression of fibrosis-associated genes than other macrophage subsets at homeostasis. Moreover, the expression of these fibrosis-associated genes increased in Gpnmb RecAM in both the LPS and bleomycin models in parallel, only diverging at day 14/15.

Interestingly, analysis of the fibrotic feature score at each time point in each model for the remaining macrophage clusters revealed a similar pattern to that observed in Gpnmb RecAM (Supplemental Figure 5). While fibrotic feature scores were much lower in the other macrophage clusters overall compared with Gpnmb RecAM, within each cluster, the scores were similar between LPS and bleomycin at days 3 and 6/7 and only diverged at day 14/15 for most clusters. This suggests that expression of genes in the fibrotic features list is not unique to fibrosis but rather represents a global response of macrophages to tissue injury or inflammation.

Given these findings, we hypothesized that homologs to the murine Gpnmb RecAM subset would be present in humans with both fibrotic and nonfibrotic lung disease. To simultaneously test this hypothesis and validate that Gpnmb RecAM corresponded to “profibrotic” macrophages described by others, we generated a Gpnmb RecAM gene signature using cluster-specific conserved markers (Supplemental Table 1). We next tested markers of macrophage subsets previously identified in human IPF lungs for enrichment of both the Gpnmb RecAM gene signature and the fibrotic features signature (49, 50). Two AM clusters from the human IPF dataset were enriched for both the Gpnmb RecAM gene signature and the fibrotic features signature (Figure 4D). The authors identified cluster 1 in this dataset as profibrotic (29). This suggests that Gpnmb RecAM share common markers with so-called profibrotic macrophages and that a Gpnmb RecAM-like macrophage subset is present in human IPF.

Although recruited macrophage numbers are low in health, a small population of macrophages expressing profibrotic genes such as SPP1 has been described in BAL from humans (51, 52). Because Gpnmb RecAM had higher expression of the fibrotic features relative to other macrophages at homeostasis, we hypothesized that Gpnmb RecAM corresponded to a BAL macrophage subset from healthy humans. Indeed, enrichment analysis revealed that genes that define the SPP1hi macrophage cluster from healthy humans were enriched for both fibrotic feature genes and Gpnmb RecAM genes (Figure 4E) (52). Thus, macrophages with these gene signatures exist in small numbers at baseline in humans and in mice. This demonstrates a clear limitation in the utility of “fibrotic feature” genes to indicate fibrosis. The presence of a macrophage subset enriched for “profibrotic” genes during health further suggests that this subset is not unique to fibrosis nor is it sufficient to cause fibrosis. Because Gpnmb RecAM gene expression overlaps with “fibrotic” cluster gene signatures but not fibrotic repair outcomes, these signatures may instead identify a reparative subset involved in both tissue homeostasis and a general response to injury.

To test this hypothesis, we assessed whether Gpnmb RecAM-like macrophages could be found in other nonfibrotic human diseases and mouse models. We calculated enrichment scores for both the Gpnmb RecAM gene signature and the fibrotic features gene signature in marker lists from published scRNA-Seq datasets from 2 distinct forms of human lung disease (COVID-19 and asthma), a mouse model of live Pneumocystis lung infection, and mouse macrophages isolated from skin wounds of healthy and diabetic mice (Supplemental Table 3) (24, 29, 52–54). The Gpnmb RecAM gene signature had significant enrichment in monocyte-derived macrophages (MoAM3) and SARS-CoV-2–infected RAM (TRAM2) in BAL from patients with severe COVID-19 (Figure 4F). Since severe COVID-19 can result in pulmonary fibrosis, we sought to compare macrophages from a disease that is not associated with interstitial fibrosis (25, 26, 54). We therefore compared macrophages from bronchial brushings of patients with allergies and asthma against patients without allergies who have asthma (55). Gpnmb RecAM genes were enriched in the markers for an SPP1-expressing monocyte-macrophage subset, as were the fibrotic features genes (Figure 4G). Similarly, Gpnmb RecAM and fibrotic features gene signatures were significantly enriched in macrophage subsets from mice with nonfibrotic lung injury from Pneumocystis jirovecii (Figure 4H) and sterile skin wounds (Figure 4I). Collectively, these data suggest a paradigm where the core biology regulating macrophage recruitment and maturation in response to injury is conserved across species and tissues. The most easily identifiable signature genes, including Spp1 and Gpnmb, mark a macrophage subset with a shared injury response identity that has been mischaracterized as uniquely or innately profibrotic.

Gpnmb RecAM transcriptional profiles differ between LPS and bleomycin. Since the presence of Gpnmb RecAM is not sufficient to predict repair outcome, we hypothesized that the conserved injury response signature driving Gpnmb RecAM clustering might hide subtler model-specific transcriptional differences important to fibrosis. To uncover transcriptional changes that might contribute to fibrotic versus nonfibrotic repair outcomes, we tested for differences in macrophage gene expression between LPS and bleomycin models at corresponding time points within each cluster. Numbers of DEGs between LPS- versus bleomycin-derived macrophages were relatively low for all clusters at day 3 (Figure 5A). However, the number of DEGs increased substantially for most clusters at day 6/7, particularly Gpnmb RecAM and Ear1int RAM. These data suggest that much of the initial macrophage injury response is conserved between models before diverging at later time points.

Differential gene expression in Gpnmb RecAM from LPS versus bleomycin. (A) Number of DEGs between LPS and bleomycin within each cluster at corresponding time points (FDR < 0.05). (B) Sankey plot of DEGs from Gpnmb RecAM at each comparison time point. Significance is based on logFC > 0.5 and FDR < 0.05. (C) Volcano plot of differentially expressed genes (DEGs) for Gpnmb RecAM LPS day 6 versus bleomycin day 7. (D) Cytoscape network visualization of Gpnmb RecAM pathway analysis performed on DEGS up in bleomycin day 7 versus up in LPS day 6. Circles represent enriched pathways and are clustered by similarity. Lines connecting the circles represent genes that overlap between pathways. Circle halves are shaded from grey (no pathway enrichment) to red (high enrichment) with left sides representing LPS and right sides representing bleomycin. Line colors mark the primary group showing significant pathway enrichment, either bleomycin (green) or LPS (purple). (E) Heatmap of transcription factor activity inference scores that were significantly different between Gpnmb RecAM from bleomycin day 7 versus LPS day 6. Only the top 8 transcription factors with the lowest adjusted P values for each injury model are shown. (F) Top 10 GO pathways enriched in the 230 DEGs upregulated in Gpnmb RecAM from bleomycin at both day 7 and day 14 compared with LPS day 6 and 15. Adjusted P < 0.05.

Because Gpnmb RecAM demonstrated enrichment for fibrosis-associated genes (Figure 4, A–C), we interrogated the LPS versus bleomycin DEG list for genes from the fibrotic features list. Of the 20 genes in the fibrotic features list, only Spp1 and Emp1 were in the top 100 DEGs increased in bleomycin relative to LPS at every time point. Six of 20 were significantly increased in bleomycin at day 6/7, and 12 of 20 were increased at day 14/15 compared with LPS (Supplemental Table 4).

We next sought to better understand Gpnmb RecAM DEGs across time. Overall, only 10 genes were upregulated in bleomycin at all 3 time points, and most of the DEGs at day 6/7 did not remain differentially expressed at day 14/15 (Figure 5B). Since DEG numbers were greatest in Gpnmb RecAM at days 6/7, we next focused on this time point. Gpnmb RecAM from bleomycin-treated mice had greater expression of chemokines associated with fibrosis, including Ccl7, Ccl17, Ccl2, and Ccl9 (56). In comparison, Gpnmb RecAM from LPS-treated mice had higher expression of genes associated with RAM identity, including Ear1, Car4, and Plet1 (Figure 5C and Supplemental Table 5).

To determine the differences in putative functions of Gpnmb RecAM from LPS- versus bleomycin-treated mice at days 6/7, we performed pathway analysis using DEGs that were increased in each model (Figure 5D and Supplemental Table 6). Here we found that LPS-derived cells were enriched for phospholipid and lipid metabolism, suggesting a role for the GM-CSF/PPARγ axis and perhaps ongoing conversion to a homeostatic RAM-like state. LPS-derived Gpnmb RecAM were also enriched for pathways related to antigen processing and tissue development, which are also indicative of homeostatic functions. By contrast, Gpnmb RecAM from bleomycin-treated mice were enriched for numerous inflammation and stress-related pathways such as mast cell activation, unfolded protein response, and response to ROS. While we previously removed actively proliferating cell clusters from the scRNA-Seq dataset, we found enrichment for cell cycle and mitosis pathways suggesting recent proliferation. This suggests that proliferation may contribute to continued expansion of the Gpnmb RecAM pool in bleomycin.

To determine putative transcription factors responsible for differences in gene expression, we performed transcription factor activity inference analysis for Gpnmb RecAM from LPS day 6 versus bleomycin day 7 (Figure 5E). LPS-derived Gpnmb RecAM were found to have relatively higher activation of transcription factors associated with lipid homeostasis and negative regulation of inflammation, including Pparg, Klf15, and Arid5b. Pparg is widely recognized as a key transcription factor that regulates RAM identity and lipid homeostasis, whereas Klf15 and Arid5b have been implicated in suppressing inflammation (57, 58). Transcription factors with increased predicted activity in Gpnmb RecAM from bleomycin relative to LPS included Hoxa11, Msx1, and Dlx5 (Supplemental Table 7). Hoxa11 and Msx1 have been shown to increase profibrotic factors such as PDGF and TGF-β (59, 60). Dlx5 has been found to bind to and suppress PPARγ activity in mesenchymal stem cells, which, if it occurs in RecAM, could mediate inhibition of RAM-like programming (61, 62).

These differences suggest that day 6/7 may represent a point of divergence in nonfibrotic versus fibrotic repair. As a final step, we identified genes that were consistently upregulated in bleomycin-derived Gpnmb RecAM at both days 7 and 14 relative to LPS days 6 and 15, hypothesizing that these might reflect gene signatures involved in the transition to fibrosis and related to the transcription factors from day 6/7. Of the 1,699 DEGs upregulated in bleomycin-derived Gpnmb RecAM at day 6/7, only 230 genes were also upregulated at day 14/15 (Supplemental Table 8). GO pathway analysis demonstrated enrichment for IFN production, chemotaxis, and cell survival (Figure 5F and Supplemental Table 8).

Taken as a whole, these analyses suggest that an additional, subtler layer of programming exists beneath the shared injury response that drives Gpnmb RecAM identity. Notably, examination of the 20 fibrotic feature genes showed that only Spp1 and Emp1 identified model-specific differences between Gpnmb RecAM at every time point, again highlighting that these genes mark a conserved injury response but largely fail to recognize biology correlated with fibrotic outcome. Bleomycin-derived Gpnmb RecAM showed increased expression of proinflammatory genes and increased activity of profibrotic transcription factors relative to LPS-derived cells, while LPS-derived Gpnmb RecAM showed greater evidence of homeostatic and antiinflammatory gene expression and transcription factor activity.