Gene-selective transcription promotes the inhibition of tissue reparative macrophages by TNF

Abstract

Anti-TNF therapies are a core anti-inflammatory approach for chronic diseases such as rheumatoid arthritis and Crohn’s Disease. Previously, we and others found that TNF blocks the emergence and function of alternative-activated or M2 macrophages involved in wound healing and tissue-reparative functions. Conceivably, anti-TNF drugs could mediate their protective effects in part by an altered balance of macrophage activity. To understand the mechanistic basis of how TNF regulates tissue-reparative macrophages, we used RNAseq, scRNAseq, ATACseq, time-resolved phospho-proteomics, gene-specific approaches, metabolic analysis, and signaling pathway deconvolution. We found that TNF controls tissue-reparative macrophage gene expression in a highly gene-specific way, dependent on JNK signaling via the type 1 TNF receptor on specific populations of alternative-activated macrophages. We further determined that JNK signaling has a profound and broad effect on activated macrophage gene expression. Our findings suggest that TNF’s anti-M2 effects evolved to specifically modulate components of tissue and reparative M2 macrophages and TNF is therefore a context-specific modulator of M2 macrophages rather than a pan-M2 inhibitor.

FADD- and RIPK3-mediated cell death ensures timely clearance of wound macrophages and promotes wound healing

“…Secondly, we demonstrate that TNF blockade in FADD MKO RIPK3 -/- mice is associated with attenuated expression of pro- inflammatory mediators and enhanced expression of pro-repair programs in late-stage wound macrophages. Recently, we reported similar effects of TNF blockade in wound healing in healthy mice, indicating that TNF suppressive-M2 effects are also present in FADD MKO RIPK3 -/- mice (Dichtl, 2022). Third, we propose that improved wound healing in FADD MKO RIPK3 -/- mice after ETA treatment is achieved not only through the reactivation of the suppressed repair phenotype, but also through an increased absolute number of late-stage pro-repair wound macrophages.…”

“…Different mechanisms contribute to resolution of inflammation in damaged and inflamed tissues (Chen, 2015; Knipper, 2015; Bosurgi, 2017; Zhang, 2019). The current view is that in most repairing tissues, including the skin, inflammatory monocytes/macrophages (Ly6C high ) undergo a phenotypic switch from a pro-inflammatory towards an anti-inflammatory phenotype (Willenborg, 2012; Knipper, 2015; Willenborg, 2021; Sanin, 2022). In addition, monocytic cells can be cleared through lymphatic drainage (Harmsen, 1985; Bellingan, 1996), recently described trans-differentiation (Meng, 2016; Sinha, 2018; Haider, 2019; Li, 2021), and/or cell death (Desmoulière, 1995; Kuhlmann, 2001; Janssen, 2011; Gautier, 2013; Moriwaki, 2014; Wu, 2014; Bleriot, 2015; Legrand, 2019).…”

“…By transcriptional profiling of early and late-stage wound macrophages we recently uncovered that early stage/type-1 towards late stage/type-2 macrophage activation dynamics are paralleled by TNF-related activation profiles (Willenborg, 2021; Sanin, 2022). Particularly early stage wound macrophages revealed a TNF-mediated cell death associated gene profile including increased expression of Tnf, Ripk1, Fadd, Ripk3, Mlkl (Willenborg, 2021; Sanin, 2022). Based on these findings, we hypothesized an important role for regulated extrinsic cell death in wound macrophages contributing to resolution of inflammation and repair.…”

Senescent cells suppress macrophage-mediated corpse removal via upregulation of the CD47-QPCT/L axis

“…Murine BMDMs: Mouse bone marrow was obtained by flushing femurs and tibiae with PBS followed by differentiation into BMDMs by culturing in complete Dulbecco’s modified Eagle’s medium (DMEM; 41966-029; Thermo Fisher Scientific) composed of 10% fetal bovine serum (S0115; Biochrome), penicillin-streptomycin, and recombinant human CSF1 (50 ng/ml) for 7 d as previously described ( Dichtl et al, 2022 ). Human MDMs : All experiments with blood from human volunteer donors were approved by the blood donation service from Boehringer Ingelheim Pharma GmbH and Co. KG following ethical standards and local regulation.…”

Neuroinflammation in retinitis pigmentosa: Therapies targeting the innate immune system

“…Benoot et al evaluated the numerous contradictory findings of TNFa application in lung cancer (138), bringing to our awareness the varied functions of various TNF family members and the positive impacts of TNF signaling. Modern genomic, transcriptomic, and proteomic techniques are useful for identifying signaling events and molecules in signal transduction (139,140). Tanzer et al (141) discussed in detail how modern proteomic approaches offer a novel perspective on TNF signaling.…”