Rewiring the bone marrow: Evolution and the transcriptional architecture of trained immunity

Emergency myelopoiesis (EM) is believed to be an essential component of hematopoietic reprogramming. In general terms, it is defined as a reactive homeostatic response of HSPCs to increased myeloid cell demand (Manz and Boettcher, 2014). EM is therefore a central feature of systemic bacterial infections (Manz and Boettcher, 2014), and viral infections, such as COVID-19 (Schulte-Schrepping et al., 2020), which induce widespread inflammation and the depletion of neutrophils as they infiltrate into tissues. Noninfectious, iatrogenic causes such as myeloablative chemotherapy can also act as triggers of HSC proliferation and myeloid cell regeneration (Pietras et al., 2016), demonstrating that the mere act of myeloid cell depletion in the absence of infection is sufficient to drive this response. Mechanistically, peripheral signals of myeloid cell demand cause usually dormant, pluripotent long-term HSCs (LT-HSCs) to expand and give rise to myeloid-biased multipotent progenitors (MPPs). EM also involves the entry of normally quiescent lineage-committed granulocyte-monocyte precursors (GMPs) into the cell cycle (Swann et al., 2024). These events are largely thought to be coordinated by the action of key cytokines, including G-CSF, GM-CSF, M-CSF, IL6, IL-1β, TNFα, TGFβ, and type I and type II interferons (Manz and Boettcher, 2014; Park et al., 2024; Pascutti et al., 2016; Swann et al., 2024), although other cytokines, including IL4, have also been shown to coordinate EM under certain circumstances (LaMarche et al., 2024). Signaling by cytokines, either in combination or in isolation, results in cell proliferation at multiple points in the hematopoietic hierarchy, as well as the activation of lineage-determining TFs such as PU.1 (Heinz et al., 2010) and CEBPβ (Hirai et al., 2006), which bias stem cells toward the myeloid lineage (de Laval et al., 2020; Pietras et al., 2016; Yamashita and Passegué, 2019).

We believe that these processes, usually perceived as transient changes enabling the temporary mobilization of monocytes and granulocytes in times of need, are essential in the induction of persistent hematopoietic reprogramming and that cytokine-induced EM serves as a necessary, but likely not sufficient, trigger of hematopoietic reprogramming. In support of this hypothesis, our review of the literature (see examples below) has consistently demonstrated that an initial EM response precedes hematopoietic reprogramming. Most stimuli lead to the upregulation of at least one identifiable cytokine among IL1β, IFNγ, or IL6 (Chavakis et al., 2022; Chavakis et al., 2019; Zhao et al., 2014)—one possible exception being LPS which may directly act on HSCs via Toll-like receptor signaling (Chavakis et al., 2019; de Laval et al., 2020). Even so, TLR ligation is believed to lead to the production of cytokines such as IL6, which feedback to partially instruct EM via paracrine signaling (Chavakis et al., 2019; Zhao et al., 2014). In general, we find that differences in hematopoietic reprogramming between stimuli can be, to some extent, predicted by the cytokines they produce (Table 1).

Cytokine-induced hematopoietic reprogramming.

The table includes stimuli of hematopoietic reprogramming from studies for which cytokines were directly investigated. The phenotype-defining cytokine is bolded. Rows are colored according to cytokine (red—IL1β, yellow—IL6 ± IFN, blue—IFN in the absence of IL6). Stimuli that induce similar cytokine repertoires also produce similar reprogramming effects.

StimulusSpecies studiedTypeKey cytokines inducedPersistent reprogramming outcomeReferencesβ-GlucanMiceInfectious mimic (PRR agonist) and inflammasome activatorIL-1β, G-CSFInherent LT-HSC myeloid bias; trained EM response to chemotherapyMitroulis et al., 2018LIPMiceSterile inflammationIL-1β, G-CSFInherent LT-HSC myeloid bias; trained EM response to LPS;
primed monocyte and neutrophil TNFα/IL-6 secretion upon LPS challengeLi et al., 2022BCG vaccinationMiceLive attenuated infectionIFN-γIncreased macrophage antimicrobial activity; IFN-γ dependentKaufmann et al., 2018COVID-19 infectionHumanViral infectionIL-6Lasting monocyte chromatin remodeling and priming; persistent GMP expansion; reversed by IL-6 blockadeCheong et al., 2023Western dietMiceMetabolic triggerIL-6, IFN-γ, IL-1β, G-CSF, GM-CSFLasting monocyte priming; GMP chromatin remodeling, differential gene expression, monocyte skewingChrist et al., 2018

β-Glucan and ligature-induced periodontitis (LIP), for example, are seemingly unrelated mouse models of hematopoietic reprogramming. Both, however, induce IL1β and similar hematopoietic reprogramming phenotypes. β-Glucan and LIP both induce a persistent myeloid bias at the level of LT-HSCs that is transplantable into naïve recipients and prime the hematopoietic system to more rapidly increase myeloid cell production in response to secondary challenges with either chemotherapy or LPS. Blockage of IL1β signaling abrogates the reprogramming of long-lived myeloid bias in response to β-glucan (Mitroulis et al., 2018) and in the model of LIP also reduces the primed secretion of TNFα and IL6 by LIP-bone marrow-derived neutrophils and monocytes in response to LPS (Li et al., 2022). In further support of the essential role of IL1β in encoding these responses at the level of LT-HSCs, studies have shown that IL1β itself is sufficient to drive the expression of PU.1, as well as macrophage colony-stimulating factor (M-CSF) and granulocyte-macrophage colony-stimulating factor (GM-CSF) within long-term hematopoietic stem cells (LT-HSCs) to drive an intrinsic myeloid bias (Pietras et al., 2016) at the very apex of the hematopoietic hierarchy.

Other stimulus-cytokine pairs further support the notion that the action of cytokines dictates hematopoietic reprogramming. In contrast to IL1β, inducers of IFNγ and IL6 appear to generate a hematopoietic reprogramming phenotype that more predominantly involves monocyte- (rather than neutrophil) skewed myeloid cell production and GMP/monocyte-centric reprogramming.

For example, vaccination with Bacillus Calmette-Guérin (BCG), a live attenuated version of Mycobacterium bovis, induces hematopoietic reprogramming in a manner that is dependent on IFNγ (Kaufmann et al., 2018). In line with IFNγ’s intrinsic ability to polarize the bone marrow toward monocyte over granulocyte production, the main hematopoietic reprogramming phenotype of BCG is the production of macrophages with an increased ability to resist Mycobacterium tuberculosis infection in vitro even in mice treated with antibiotics, an effect which is lost completely in IFNγR KO mice (Kaufmann et al., 2018).

COVID-19 induces hematopoietic reprogramming via a mechanism that appears to involve IL6. Often acting in concert with IFNγ, IL6 acts directly on MPPs by downregulating production of the TFs Cebpa and Runx1, thus further skewing downstream GMPs toward the monocyte lineage (de Bruin et al., 2012). Accordingly, COVID infection can induce the persistence of elevated GMPs detected in the peripheral circulation for at least 4–12 months following exposure and leads to the production of epigenetically modified monocytes primed to secrete elevated levels of IL6 and TNF-α in response to TLR7/8 agonist R848 or IFNα (Cheong et al., 2023). Treatment with Tocilizumab—an antibody which blocks IL6 signaling—leads to significantly reduced levels of the GMPs. Moreover, in a mouse model of COVID infection, concomitant treatment with anti-IL6 significantly decreased the post-COVID burden of inflammatory myeloid cells within both the lungs and brain (Cheong et al., 2023).

Western diet is an interesting example of a stimulus that induces multiple cytokines simultaneously, including IL6, IFNγ, and IL1β. In line with the tendency for IL6 and IFNγ to reprogram HSPCs at the level of the GMP and monocyte, western diet hematopoietic reprogramming is also characterized by lasting effects on the chromatin accessibility and gene profiles of GMPs isolated even 4 weeks after return to a control diet, GMP skewing toward the monocyte lineage, and priming of both monocytes and GMPs. Although IL1β was markedly increased in this study, whether its effects on LT-HSCs resembled those of other IL1β producers, such as β-glucan, remains unclear (Christ et al., 2018).

Altogether, the data suggest that the specific flavor of hematopoietic reprogramming that is induced by any given stimulus is influenced by the cytokines which they induce (Table 1). β-Glucan and LIP converge on IL-1β and in both examples, result in LT-HSCs with persistent myeloid bias and primed EM response to secondary challenges (Li et al., 2022; Mitroulis et al., 2018). Mycobacteria, which induce the monocyte/macrophage-polarizing cytokine IFNγ when injected intravenously, train the bone marrow of mice to give rise to macrophages with increased bacterial killing capacity (Kaufmann et al., 2018). Models of human COVID infection and western diet in mice implicate IL-6 as a key cytokine in reprogramming the bone marrow at the level of monocytes and GMPs (Cheong et al., 2023; Christ et al., 2018). When taken together, existing data suggests that blocking the signaling of key cytokines involved in programming demand-adapted myeloid cell mobilization abrogates both EM and the ability of the hematopoietic system to become reprogrammed, suggesting that EM may be a necessary component of hematopoietic reprogramming. In some cases, administration of recombinant cytokines, such as IFNγ (Kain et al., 2023), has also reproduced phenotypes of hematopoietic reprogramming, thereby also suggesting sufficiency. Nonetheless, there remains a need for more systematic necessity and sufficiency experiments to further delineate the exact role of each EM-inducing cytokine in hematopoietic reprogramming.