Juan Luis Mendoza

Cytokine receptors signal through a dedicated Janus kinase (JAK) that is thought to be constitutively bound to the receptor intracellular domain (ICD). We tested this one-receptor, one-JAK model biophysically. A bead-based screen of JAK1 and TYK2 against 32 receptor ICDs, confirmed by microscale thermophoresis to measure affinity, revealed dissociation constants spanning tens of nanomolar to tens of micromolar, indicating that many interactions are not high-affinity and may not be constitutive. Binding was also widely cross-reactive: GMCSFRα bound both JAK1 and TYK2, and IL2Rβ bound TYK2 far more tightly than JAK1. In cells, GM-CSF signaled through JAK1 when JAK2, JAK3, and TYK2 were inhibited. JAK–receptor pairing is therefore permissive and graded rather than exclusive and constitutive.

Type III interferon (IFN3, IFNλ) drives antiviral defense at epithelial barriers with a more favorable safety profile than Type I interferon (IFN1), but weaker signaling limits its therapeutic potential. To identify small molecules that potentiate IFN-JAK-STAT signaling, we developed a high-throughput live-cell assay measuring STAT1/STAT2 phosphorylation in A549 cells and screened ∼8,640 compounds. This identified proteasome inhibitors (MG132, delanzomib, ixazomib, oprozomib, bortezomib) as selective potentiators of IFN3-induced STAT activation, with minimal effect on IFN1 signaling. Proteasome inhibition enhanced IFN3 antiviral activity to levels approaching IFN1. Mechanistically, proteasome inhibition increased cell-surface IL10Rβ, the limiting IFN3 receptor subunit, thereby increasing receptor JAK-STAT signaling. It did not alter IFN1 receptor levels but protected IFNAR2 from late ligand-induced downregulation. These findings establish receptor subunit availability as a rate-limiting, druggable node governing IFN3 signaling strength and demonstrate a scalable platform for identifying cytokine-selective signaling potentiators, with implications for mucosal antiviral therapeutics.

Cytokines signal by bringing receptor subunits together, but the role of receptor geometry in shaping signaling remains unclear because natural ligands enforce fixed assemblies. Here, we present a de novo protein design platform that rigidly scaffolds receptor-binding domains into defined spatial arrangements. Applying this across IL-7, type I and III interferons, IL-10, gp130, β common, and synthetic receptor pairs, we show that by varying geometry, we can bias pSTAT pathway usage and tune functional outcomes. Geometric control allowed us to decouple pSTAT1 from pSTAT5 in IL-7, separate antigen presentation (MHC-I) from checkpoint induction (PD-L1) in type I interferons, and suppress pro-inflammatory IFNγ secretion while retaining anti-inflammatory activity in IL-10. We further created minimal IL-6 and IL-3 agonists and strengthened synthetic receptor pairings inaccessible with present cytokines. These results establish receptor geometry as a central determinant of cytokine activity and provide a platform for programmable immune modulation.

IFNλ4 has posed a conundrum in human immunology since its discovery in 2013, with its expression linked to complications with viral clearance. While genetic and cellular studies revealed the detrimental effects of IFNλ4 expression, extensive structural and functional characterization has been limited by the inability to express and purify the protein, complicating explanations of its paradoxical behavior. In this work, we report a method for robust production of IFNλ4. We then use yeast surface display to affinity-mature IL10Rβ and solve the 72 kilodalton structures of IFNλ4 (3.26 Å) and IFNλ3 (3.00 Å) in complex with their receptors IFNλR1 and IL10Rβ using cryogenic electron microscopy. Comparison of the structures highlights differences in receptor engagement and reveals a distinct 12-degree rotation in overall receptor geometry, providing a potential mechanistic explanation for differences in cell signaling, downstream gene induction, and antiviral activities. Further, we perform a structural analysis using molecular modeling and simulation to identify a unique region of IFNλ4 that, when replaced, enables secretion of the protein from cells. These findings provide a structural and functional understanding of the IFNλ4 protein and enable future comprehensive studies towards correcting IFNλ4 dysfunction in large populations of affected patients.

Netrins dictate attractive and repulsive responses during axon growth and cell migration, where the presence of the receptor Uncoordinated-5 (UNC-5) on target cells results in repulsion. Here, we showed that UNC-5 is a heparin-binding protein, determined its structure bound to a heparin fragment, and could modulate UNC-5–heparin affinity using a directed evolution platform or structure-based rational design. We demonstrated that UNC-5 and UNC-6/netrin form a large, stable, and rigid complex in the presence of heparin, and heparin and UNC-5 exclude the attractive UNC-40/DCC receptor from binding to UNC-6/netrin to a large extent. Caenorhabditis elegans with a heparin-binding–deficient UNC-5 fail to establish proper gonad morphology due to abrogated cell migration, which relies on repulsive UNC-5 signaling in response to UNC-6. Combining UNC-5 mutations targeting heparin and UNC-6/netrin contacts results in complete cell migration and axon guidance defects. Our findings establish repulsive netrin responses to be mediated through a glycosaminoglycan-regulated macromolecular complex.

Type I and III Interferons (IFN) constitute the host system’s first line of defense against viral infections. Although the two families use distinct extracellular receptor complexes, an identical pair of Janus kinases (JAK) activates a similar set of signal transducer and activator of transcription (STATs) through a conserved pathway. Consequently, type I and III IFNs are presumed to activate a largely overlapping set of IFN-stimulated genes (ISGs) and elicit similar biological responses. Therapeutically, type III IFNs are attractive alternatives to type I IFNs due to their innate tissue specificity and lower systemic toxicity. However, a major limitation of type III IFNs is the significantly lower potency of their physiological activities compared to type I IFNs. To evaluate the role of receptor geometry in IFN signaling, we engineered cell lines that express wild-type and mutant IFNλ receptors (IFNλR1) with rotated intracellular registers with respect to the associated JAK1. Evaluation of downstream signaling and biological activity of type III IFNs in cells with varied JAK-JAK geometries uncovered variant receptors that result in potentiation of type III IFN signaling and all downstream activities. With the combined use of a high-affinity ligand to stabilize the extracellular receptor complex, we found that the optimization of the intracellular JAK-JAK geometry enhances the type III IFN antiviral and anti-proliferative activities by 2- and 3-logs, respectively. In addition to providing a molecular basis for the observed differences in potency between type I and III IFNs, this work provides deeper insights into broader cytokine signaling mechanisms and novel blueprints for modulating cytokine functions to develop next generation antiviral and anticancer therapeutics.