Innate immunity triggers responsible for viral control or hyperinflammation in COVID‐19 are largely unknown. Here we show that the SARS‐CoV‐2 spike protein (S‐protein) primes inflammasome formation and release of mature interleukin‐1β (IL‐1β) in macrophages derived from COVID‐19 patients but not in macrophages from healthy SARS‐CoV‐2 naïve individuals. Furthermore, longitudinal analyses reveal robust S‐protein‐driven inflammasome activation in macrophages isolated from convalescent COVID‐19 patients, which correlates with distinct epigenetic and gene expression signatures suggesting innate immune memory after recovery from COVID‐19. Importantly, we show that S‐protein‐driven IL‐1β secretion from patient‐derived macrophages requires non‐specific monocyte pre‐activation in vivo to trigger NLRP3‐inflammasome signaling. Our findings reveal that SARS‐CoV‐2 infection causes profound and long‐lived reprogramming of macrophages resulting in augmented immunogenicity of the SARS‐CoV‐2 S‐protein, a major vaccine antigen and potent driver of adaptive and innate immune signaling.

Aging is accompanied by a general decline in the function of many cellular pathways. However, whether these are causally or functionally interconnected remains elusive. Here, we study the effect of mitochondrial–nuclear communication on stem cell aging. We show that aged mesenchymal stem cells exhibit reduced chromatin accessibility and lower histone acetylation, particularly on promoters and enhancers of osteogenic genes. The reduced histone acetylation is due to impaired export of mitochondrial acetyl-CoA, owing to the lower levels of citrate carrier (CiC). We demonstrate that aged cells showed enhanced lysosomal degradation of CiC, which is mediated via mitochondrial-derived vesicles. Strikingly, restoring cytosolic acetyl-CoA levels either by exogenous CiC expression or via acetate supplementation, remodels the chromatin landscape and rescues the osteogenesis defects of aged mesenchymal stem cells. Collectively, our results establish a tight, age-dependent connection between mitochondrial quality control, chromatin and stem cell fate, which are linked together by CiC.

Stem cell differentiation is accompanied by increased mRNA translation. The rate of protein biosynthesis is influenced by the polyamines putrescine, spermidine and spermine, which are essential for cell growth and stem cell maintenance. However, the role of polyamines as endogenous effectors of stem cell fate and whether they act through translational control remains obscure. Here, we investigate the function of polyamines in stem cell fate decisions using hair follicle stem cell (HFSC) organoids. Compared to progenitor cells, HFSCs showed lower translation rates, correlating with reduced polyamine levels. Surprisingly, overall polyamine depletion decreased translation but did not affect cell fate. In contrast, specific depletion of natural polyamines mediated by spermidine/spermine N1-acetyltransferase (SSAT; also known as SAT1) activation did not reduce translation but enhanced stemness. These results suggest a translation-independent role of polyamines in cell fate regulation. Indeed, we identified N1-acetylspermidine as a determinant of cell fate that acted through increasing self-renewal, and observed elevated N1-acetylspermidine levels upon depilation-mediated HFSC proliferation and differentiation in vivo. Overall, this study delineates the diverse routes of polyamine metabolism-mediated regulation of stem cell fate decisions. This article has an associated First Person interview with the first author of the paper.

31Ageing is accompanied by a general decline in the function of many cellular pathways, with 32 metabolic alterations, epigenetic modifications, and stem cell exhaustion representing three 33 important hallmarks of the ageing process. However, whether these pathways are causally or 34 functionally related at a molecular level remains poorly understood. Here, we use bone 35 marrow-derived mesenchymal stem cells (MSCs) isolated from young and old mice to address 36 how age-dependent changes in metabolism and epigenetics are linked and how they impact 37 on the ageing transcriptome and differentiation potential. Given that MSCs maintain specific 38 age-associated properties even under prolonged culture conditions, such as the age-39 dependent decrease in osteogenic differentiation, they are an excellent model to investigate 40 in vitro the connection of ageing hallmarks on a mechanistic level. In this study, we 41 demonstrate that upon ageing, osteogenic potential of MSCs declines as a consequence of 42 deregulated mito-nuclear communication, mediated by decreased levels of the citrate carrier 43 (CiC). Age-dependent down-regulation of CiC results in acetyl-CoA trapping within 44 mitochondria, hypo-acetylation of histones and chromatin compaction. Together, these 45 changes lead to an altered transcriptional output and are responsible for the reduced 46 differentiation capacity into osteoblasts. Strikingly, short-term supplementation of aged cells 47 with acetate, an exogenous source for cytosolic acetyl-CoA production, rescues not only the 48 age-associated reduction of histone acetylation, but also the osteogenesis defect, 49 representing a potential target for in vitro MSC rejuvenation. 50 51 52 53 54 55 56 57 58 59 60 61 Stem cell exhaustion, a result of reduced self-renewal capacity and imbalanced differentiation 62 potential, is a well-established hallmark of the ageing process (López-Otín et al. 2013). Bone 63 marrow mesenchymal stem cells (MSCs) have been shown to play an important role upon 64 ageing due to their ability to regenerate bone by giving rise to adipocytes, chondrocytes and 65 osteoblasts (Dominici et al. 2006; da Silva Meirelles, Caplan, and Nardi 2008; Caplan 2008). 66 Aged MSCs show decreased capacity to differentiate into the osteogenic and chondrogenic 67 lineages. This feature has been linked to increased fat content in the bone marrow upon 68 ageing and concomitantly higher risk of osteoporosis and fractures (Kim et al. 2012; S. Zhou 69 et al. 2008). This change in fate commitment is also known to occur in other stem cell 70 populations upon ageing, such as hematopoietic stem cells, which show a biased 71 differentiation potential towards the myeloid lineage (Akunuru and Geiger 2016). 72 Chromatin architecture influences stem cell fate decisions and cell differentiation is often 73 accompanied by chromatin re-arrangements (Dixon et al. 2015). Research over the last few 74 years has revealed that ageing manifests itself -among others -by changes in chromatin 75 architecture and subsequentl...

Bone‐derived mesenchymal stem cells (MSCs) reside in a hypoxic niche that maintains their differentiation potential. While hypoxia (low oxygen concentration) was reported to critically support stem cell function and osteogenesis, the molecular events triggering changes in stem cell fate decisions in response to normoxia (high oxygen concentration) remain elusive. Here, we study the impact of normoxia on mitochondrial–nuclear communication during stem cell differentiation. We show that normoxia‐cultured murine MSCs undergo profound transcriptional alterations which cause irreversible osteogenesis defects. Mechanistically, high oxygen promotes chromatin compaction and histone hypo‐acetylation, particularly on promoters and enhancers of osteogenic genes. Although normoxia induces metabolic rewiring resulting in elevated acetyl‐CoA levels, histone hypo‐acetylation occurs due to the trapping of acetyl‐CoA inside mitochondria owing to decreased citrate carrier (CiC) activity. Restoring the cytosolic acetyl‐CoA pool remodels the chromatin landscape and rescues the osteogenic defects. Collectively, our results demonstrate that the metabolism–chromatin–osteogenesis axis is perturbed upon exposure to high oxygen levels and identifies CiC as a novel, oxygen‐sensitive regulator of the MSC function.