Network pharmacology of JAK inhibitors

Abstract

Small-molecule inhibitors of the Janus kinase family (JAKis) are clinically efficacious in multiple autoimmune diseases, albeit with increased risk of certain infections. Their precise mechanism of action is unclear, with JAKs being signaling hubs for several cytokines. We assessed the in vivo impact of pan-and isoform-specific JAKi in mice by immunologic and genomic profiling. Effects were broad across the immunogenomic network, with overlap between inhibitors. Natural killer (NK) cell and macrophage homeostasis were most immediately perturbed, with network-level analysis revealing a rewiring of coregulated modules of NK cell transcripts. The repression of IFN signature genes after repeated JAKi treatment continued even after drug clearance, with persistent changes in chromatin accessibility and phospho-STAT responsiveness to IFN. Thus, clinical use and future development of JAKi might need to balance effects on immunological networks, rather than expect that JAKis affect a particular cytokine response and be cued to long-lasting epigenomic modifications rather than by short-term pharmacokinetics.JAK inhibitor | tofacitinib | systems pharmacology A drug's mechanism of action usually refers to the specific molecular or biologic activity that it perturbs, and drug optimization aims at maximizing potency and specificity vs. this target. However, the molecular target may be far removed from the processes that ultimately drive the therapeutic effect. For instance, even though the target is known, it remains unclear which cell or pathway is pivotally affected by anti-PD1 during cancer immunotherapy. Given the interdependencies of cellular and molecular players in biological systems, a drug is likely to have effects far broader than its molecular target. Conversely, it may be hampered by inherent resistance to perturbation of interconnected networks. This complexity is encapsulated in the concepts of network pharmacology, which proposes that drug development focus on network-level alterations, rather than on exquisite specificity for an individual target (1).JAK kinase inhibitors (JAKis) have been intensively and successfully pursued over the last two decades (2, 3) and could be considered poster children of network pharmacology. JAK kinases (JAK1/2/3 and TYK2) are the initial mediators of signaling pathways triggered by many cytokines and hematopoietic growth factors, and activate transducers of the STAT family to prompt cell activation and phenotypic differentiation in all immunocyte lineages (4). The cytokine network is an unusually interconnected one, because cytokines can induce each other, or each other's receptors, and can enhance or stifle each other's signaling pathways. Further complexity stems from the widespread sharing of JAK kinases by cytokine receptors (e.g., JAK1 is connected to receptors for interferons,

JAK/STAT signaling in regulation of innate lymphoid cells: The gods before the guardians

“…The same effect has also been observed in patients undergoing tofacitinib treatment . In comparison to adaptive cells which remain mainly unaltered, NK cells are highly sensitive to both first‐generation of JAK inhibitors (tofacitinib and baricitinib) as well as JAK1‐ or JAK3‐specific inhibitors . Based on these observations, further studies are clearly needed to establish more appropriate dosing of these drugs in order to maximize their efficacy on specific immune responses while minimizing toxicity.…”

“…However, from a therapeutic point of view, it is interesting to note that a JAK1‐selective inhibitor is more effective in inhibiting secondary autocrine responses induced by IFN‐γ in NK cells . In vivo treatment with JAK inhibitors in animal models has been associated with a strong reduction in the NK cell frequency . The same effect has also been observed in patients undergoing tofacitinib treatment .…”

“…Transcriptomic analysis of IL‐2‐activated NK cells has shown that specific JAK3 and JAK1 inhibitors have similar effects on gene expression. However, from a therapeutic point of view, it is interesting to note that a JAK1‐selective inhibitor is more effective in inhibiting secondary autocrine responses induced by IFN‐γ in NK cells . In vivo treatment with JAK inhibitors in animal models has been associated with a strong reduction in the NK cell frequency .…”

Decoding inflammation, its causes, genomic responses, and emerging countermeasures

“…The homeostasis of NK cells and macrophages was most profoundly perturbed by JAK inhibitors with a longer lasting repression of IFN signature genes. Some of these changes persisted after the discontinuation of treatment . These findings are important as JAK inhibitors, also named Jakinibs, have significant side effects such as serious and opportunistic infections with Mycobacterium tuberculosis , Herpes zoster , Cytomegalovirus , Pneumocystis jirovecii pneumonia and other pneumonias .…”

“…Some of these changes persisted after the discontinuation of treatment. 204 These findings are important as JAK inhibitors, also named Jakinibs, have significant side effects such as serious and opportunistic infections with Mycobacterium tuberculosis, Herpes zoster, Cytomegalovirus, Pneumocystis jirovecii pneumonia and other pneumonias. 197 Thus, the suppression of autoimmune inflammation by Jakinibs may inadvertently promote the emergence of microbial inflammation.…”