Multiomics Analyses Reveal the Central Role of Pentose Phosphate Pathway in Resident Thymic Macrophages to Cope with Efferocytosis-Associated Stress

Tissue-resident macrophages (TRMs) are heterogeneous cell populations found throughout the body. Depending on their location, they perform diverse functions maintaining tissue homeostasis and providing immune surveillance. To survive and function within, TRMs adapt metabolically to the distinct microenvironments. However, little is known about the metabolic signatures of TRMs. The thymus provides a nurturing milieu for developing thymocytes yet efficiently removes those that failed the selection, relying on the TRMs – resident thymic macrophages (TMφs). This study harnesses multiomics analyses to characterize TMφs and unveils their unique metabolic features. We find that the pentose phosphate pathway (PPP) is preferentially activated in TMφs, responding to the reduction-oxidation demands associated with the efferocytosis of dying thymocytes. The blockade of PPP in Mφs leads to decreased efferocytosis, which can be rescued by ROS scavengers. Our study reveals the key role of PPP in TMφs and underscores the importance of metabolic adaptation in supporting Mφ efferocytosis. Bone-marrow-derived macrophages generated from C57BL mice were treated with or without dexamethasone-induce apoptotic thymocytes at the ratio of 1:40. After 24 hr, the apoptotic cells were removed and the macrophages were harvested for RNA extraction. Each sample represents a biological replicate. The library was prepared by using Illumina TruSeq Stranded mRNA Sample Prep Kit and sequenced by Illumina NextSeq High Output Kit v2.5-75 cycles on the NextSeq 550 platform. The sequence was annotated according to Mus musculus GRCm38 mm10.