30Macrophages are heterogeneous multifunctional leukocytes which are regulated in a tissue-and disease-31 specific context. Many different studies have been published using in vitro macrophage models to study 32 disease. Here, we aggregated public expression data to define consensus expression profiles for eight 33 commonly-used in vitro macrophage models. Altogether, we observed well-known but also novel markers 34 for different macrophage subtypes. Using these data we subsequently built the classifier macIDR, capable 35 of distinguishing macrophage subsets with high accuracy (>0.95). This classifier was subsequently applied 36 to transcriptional profiles of tissue-isolated and disease-associated macrophages to specifically define 37 macrophage characteristics in vivo. Classification of these in vivo macrophages showed that alveolar 38 macrophages displayed high resemblance to interleukin-10 activated macrophages, whereas 39 macrophages from patients with chronic obstructive pulmonary disease patients displayed a drop in 40 interferon-γ signature. Adipose tissue-derived macrophages were classified as unstimulated macrophages, 41 but resembled LPS-activated macrophages more in diabetic-obese patients. Finally, rheumatoid arthritic 42 synovial macrophages showed characteristics of both interleukin-10 or interferon-γ signatures. Altogether, 43 our results suggest that macIDR is capable of identifying macrophage-specific changes as a result of 44 tissue-and disease-specific stimuli and thereby can be used to better define and model populations of 45 macrophages that contribute to disease. 46 47 Page 3 of 23 MAIN TEXT 48 49 transcriptomic alteration associated with inflammation, infection, wound healing, and tumor growth. 64 However, compared to in vitro MDM activation, in vivo macrophage activation represents a complex and 65 dynamic process driven by multiple local factors. The most comprehensive study to date on gene 66 expression profiling of in vitro macrophages was performed by Xue et al., where the authors activated 67 MDMs under various conditions and identified distinct stimulus-specific transcriptional modules (5). Their 68 results suggested a broader view of how macrophages react upon divergent stimulation, thereby extending 69 the classical dichotomous pro-and anti-inflammatory model to an activation spectrum. While there have 70 been attempts to summarize published studies in an effort to attain consensus (4), a proper integrative 71 analysis has thus far not been performed. Furthermore, it remains unclear to what extent the in vitro 72 macrophage-models resemble their in vivo counterparts and which specific subtypes associate with 73 disease. 74In this study, we integrated 206 microarray and RNA-sequencing (RNA-seq) datasets from 19 75 different studies (7-24) ( Table 1) to systematically characterize eight different human MDM activation 76 states. First, we identified consistently differentially expressed genes (cDEGs) by comparing activated with 77 unstimulated macrophages using a random effects meta-...