This gets a little deep, but nonetheless may explain some things:
Abstract
Interferons (IFNs) are key initiators and effectors of the immune response against malignant cells and also directly inhibit tumor growth. IFNα is highly effective in the treatment of myeloproliferative neoplasms (MPNs), but the mechanisms of action are unclear and it remains unknown why some patients respond to IFNα and others do not. Here, we identify and characterize a pathway involving PKCδ-dependent phosphorylation of ULK1 on serine residues 341 and 495, required for subsequent activation of p38 MAPK. We show that this pathway is essential for IFN-suppressive effects on primary malignant erythroid precursors from MPN patients, and that increased levels of ULK1 and p38 MAPK correlate with clinical response to IFNα therapy in these patients. We also demonstrate that IFNα treatment induces cleavage/activation of the ULK1-interacting ROCK1/2 proteins in vitro and in vivo, triggering a negative feedback loop that suppresses IFN responses. Overexpression of ROCK1/2 is seen in MPN patients and their genetic or pharmacological inhibition enhances IFN-anti-neoplastic responses in malignant erythroid precursors from MPN patients. These findings suggest the clinical potential of pharmacological inhibition of ROCK1/2 in combination with IFN-therapy for the treatment of MPNs.
Introduction
Type I interferons (IFNs) are critical frontline effectors of the immune defense against pathogens and cancer1,2. Additionally, IFNs act directly on tumor cells blocking their growth, survival, migration, and other pro-tumorigenic events3. Type I IFNs exert their effects by binding to the Type I IFN receptor (IFNAR) and subsequently activating multiple signaling pathways that lead to the expression of IFN-stimulated genes (ISGs), whose protein products drive several distinct biological functions4,5,6. Extensive clinical studies using different formulations of IFN-alpha (IFNα) have demonstrated anti-tumor activity against several malignancies. IFNα treatment is especially effective in Philadelphia chromosome negative myeloproliferative neoplasms (MPNs), and has been approved by the U.S. Food and Drug Administration for the treatment of hairy cell leukemia, AIDS-related Kaposi’s sarcoma, and chronic myelogenous leukemia (CML)3,7.
MPNs are clonal hematopoietic stem cell (HSC) disorders characterized by an increased risk of bleeding, thrombosis, bone marrow fibrosis and, in some cases, transformation to acute myeloid leukemia (AML)8,9. There are three types of MPNs: polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). In 95% of MPN patients, somatic mutations in one of three genes: JAK2, CALR, or MPL occur in a single HSC, giving rise to malignant stem cells with constitutively active MPL-JAK-STAT signaling8. JAK2V617F is the most common mutation and occurs in ~95% of PV patients and 50–60% of ET and PMF patients10,11,12,13. JAK2 inhibitors are approved for the treatment of MPNs, however, overall they have a modest effect and rarely achieve complete molecular or pathologic remission14. In contrast, in recent clinical studies, pegylated IFNα (PEG-IFN) was shown to induce durable hematological and molecular responses in MPN patients, and in some cases complete remission7,15,16,17,18,19. The mechanism(s) of action of IFN in MPNs are unclear and the reason for molecular relapses, which have been reported in some patients20, are unknown.
We have previously demonstrated that Unc-51-like kinase 1 (ULK1) is required for IFN-induced anti-clonogenic effects against malignant erythroid progenitor cells from MPN patients and that ULK1 is required for IFN-mediated activation of p38 MAPK and expression of specific ISGs21. In the present study, we identify protein kinase C-delta (PKCδ) as an upstream regulator of the ULK1-p38 MAPK cascade. We also identify ROCK1/2 as interactor proteins of ULK1 and negative feedback regulators of IFNα-induced anti-neoplastic effects in primary MPN cells. Additionally, we provide evidence that increased expression of elements of the pathway correlate with clinical response to IFNα therapy in MPN patients, underscoring the importance of this signaling circuit in the IFN-system.
Results
Type I IFN treatment activates a PKCδ-ULK1-p38 MAPK signaling cascade
At the outset, we sought out the IFN-regulated signals controlling engagement of ULK1. There are putative PKCδ phosphorylation sites in ULK122 and, identified from our previous work, PKCδ activity is essential for type I IFN-induced phosphorylation of p38 MAPK and the subsequent transcription of ISGs23,24. This prompted us to investigate if PKCδ and ULK1 interact during activation of IFNAR in JAK2V617F-positive cells. In co-immunoprecipitation assays using two JAK2V617F-expressing leukemia cell lines, we found ULK1 associated with PKCδ, both before and after IFNα-treatment (Fig. 1a, b). This constitutive interaction between PKCδ and ULK1, however, was not JAK2V617F-dependent, as it was also detected in JAK2V617F-negative leukemia lines (Fig. 1c, d). These results raised the possibility that IFN could stimulate PKCδ-induced phosphorylation of ULK1. Thus, to determine whether ULK1 is a substrate for PKCδ associated with type I IFN signaling, in vitro kinase assays were conducted on anti-PKCδ immunoprecipitates, using inactive GST-ULK1 as an exogenous substrate. Our results revealed that PKCδ phosphorylates ULK1 in a type I IFN-dependent manner (Fig. 1e).
Link to Figure 1e: nature.com/articles/s41467-...
As previous studies using liquid chromatography (LC) and tandem mass spectrometry (MS/MS) have identified Ser341, Ser467 and Ser495 as the putative PKCδ phosphorylation sites in ULK122, we next generated single serine-to-alanine (S/A) ULK1 mutants (S341A, S467A and S495A) and a triple (SSS/AAA) ULK1 mutant (S341/467/495 A). ULK1 WT and Ser-to-Ala ULK1 mutants were overexpressed in HEK293T cells, immunoprecipitated from cell lysates, inactivated, and used as substrates for purified active GST-PKCδ in the presence of 32P-ATP in kinase assays (Fig. 1f). While replacement of Ser467 by Ala did not result in an obvious alteration of phosphorylation, mutation of Ser341 to Ala (S341A) and Ser495 to Ala (S495A) reduced phosphorylation of ULK1 by PKCδ (Fig. 1f). Additionally, this reduction was more evident for the triple mutant (SSS/AAA) ULK1 (Fig. 1f). These results suggest that PKCδ directly phosphorylates ULK1 on both Ser341 and Ser495 residues (Fig. 1f), which prompted us to generate two phospho-specific ULK1 antibodies, one recognizing ULK1 phosphorylated on Ser341 and the other recognizing ULK1 phosphorylated on Ser495. We confirmed the specificity of the antibodies using Ulk1/2−/− mouse embryonic fibroblasts (MEFs) transfected with myc-tagged empty vector, ULK1 WT, ULK1 S341A and ULK1 S495A mutants (Supplementary Fig. 1a, b). The p-Ser341ULK1 antibody gave a strong signal in the Ulk1/2−/− cells transfected with both ULK1 WT and ULK1 S495A mutant, but not in cells transfected with empty vector or the ULK1 S341A mutant. Likewise, the p-Ser495ULK1 antibody gave a strong signal in the Ulk1/2−/− cells transfected with both ULK1 WT and ULK1 S341A mutant, but not in the cells transfected with empty vector or ULK1 S495A mutant, confirming the specificity of these antibodies (Supplementary Fig. 1a, b). Next, using Ulk1/2+/+ MEFs, we provide evidence that phosphorylation of ULK1 on both Ser341 and Ser495 is induced by IFNα treatment (Supplementary Fig. 2). Moreover, using siRNA-mediated knockdown of PKCδ in U937 cells, we show that PKCδ expression is required for IFNα-mediated phosphorylation of ULK1 on Ser341 and Ser495, but not on Ser757, an AKT/mTOR phosphorylation site21 (Fig. 2a–c). As ULK1 is required for IFN-mediated activation of p38 MAPK, leading to transcription of ISGs21, we next sought to determine whether phosphorylation of ULK1 on Ser341 and Ser495 residues is essential for IFN-induced activation of p38 MAPK. To this end, we overexpressed myc-tagged empty vector, ULK1 WT, ULK1 S341A and ULK1 S495A in Ulk1/2−/− MEFs. These cells were then treated with IFNα and the phosphorylation of p38 MAPK was assessed. ULK1 WT, but not the ULK1 S/A mutants, could rescue IFNα-induced activation of p38 MAPK (Fig. 2d). Additionally, we overexpressed myc-tagged empty vector, ULK1 WT, ULK1 S341A and ULK1 S495A in ULK1 KO KT-1 cells. ULK1 protein expression or its absence was confirmed by anti-ULK1 immunoblotting (Supplementary Fig. 3 and Fig. 2e). The different transfected cells were then either left untreated or were treated with IFNα for 6 h and the mRNA expression of ISGs was evaluated by qRT-PCR analysis. In contrast with ULK1 S341A and ULK1 S495A, expression of the ULK1 WT substantially increased the IFNα-induced expression of IFIT1, OAS1 and IFIT3 compared to empty vector-transfected ULK1 KO KT-1 cells (Fig. 2f–h). Moreover, siRNA-mediated targeted inhibition of PKCδ expression reversed the suppressive effects of IFNα on primitive malignant erythroid precursors (Fig. 3a). Thus, as previously shown for ULK121 and p38 MAPK25, PKCδ engagement by activation of IFNAR is essential for the suppressive effects of IFNα on primary malignant PV progenitors, in vitro. Taken together these results provide evidence of previously unknown signaling events, in which activation of IFNAR controls PKCδ-mediated ULK1 phosphorylation on Ser341 and Ser495 and that ULK1 phosphorylation at these sites is required for downstream activation of p38 MAPK and transcription of ISGs.
Link to Figure 2: nature.com/articles/s41467-...
Link to Figure 3: nature.com/articles/s41467-...
To investigate whether constitutive levels of elements of this pathway may therefore discern responsiveness to IFN treatment, we examined mRNA expression levels of PKCδ, ULK1 and p38 MAPK in peripheral blood or bone marrow mononuclear cells from patients enrolled in the Myeloproliferative Disorders Research Consortium (MPD-RC)-111 study who received PEG-IFN-α2a (Pegasys) (clinical trial #NCT01259817)7 (Supplementary Table 1). Patients expressing higher pre-treatment mRNA levels of ULK1 and p38 MAPK were more likely to respond to PEG-IFN-α2a therapy (Fig. 3b), from which we infer a key role for this pathway in the anti-neoplastic effects of IFN in vivo. Future prospective clinical studies will be required to fully validate these findings and examine the potential of ULK1 and p38 MAPK as biomarkers of IFN-responsiveness.
ROCK1 and ROCK2 are overexpressed in MPN patients and interact with ULK1
Next, to identify binding partners of ULK1 in cells of MPN origin, we performed nano-LC MS/MS analysis of endogenous protein-ULK1 complexes isolated from untreated and IFNα-treated JAK2V617F-expressing HEL cells. The data indicate that ULK1 potentially interacts with 40 proteins in untreated cells, and with 38 proteins after IFNα treatment, 33 of which are identical in untreated and treated cells and 5 exclusively interact with ULK1 following IFN treatment (Supplementary Fig. 4, ProteomeXchange identifier PXD021748.). Among these five, is ROCK1 (Supplementary Fig. 4), a protein involved in promoting survival of some malignant hematopoietic cells26,27. We provide evidence that expression of both ROCK1 and, its related isoform, ROCK228, is increased in peripheral blood neutrophils from ET, PMF, and PV patients compared to age-matched healthy donors (Fig. 4a, b). Moreover, we used the DepMap Portal (depmap.org/portal/) to assess the relative protein expression of ROCK1 and ROCK2 in leukemia and other types of cancer cell lines (Supplementary Fig. 5). Interestingly, ROCK1 expression is higher in leukemia and lymphoma cell lines, compared to other types of cancer cell lines, whereas ROCK2 expression is the highest in colon cancer cells (Supplementary Fig. 5). Using co-immunoprecipitation followed by immunoblotting analyses, we found that ULK1 interacts preferentially with the cleaved/active forms of both ROCK1 and ROCK2 proteins28 in JAK2V617F-expressing cells (Fig. 4c, d).
Link to Figure 4: nature.com/articles/s41467-...
Caspases mediate cleavage and subsequent activation of ROCK1/228 and type I IFNs promote apoptosis through activation of caspases29, prompting us to examine whether IFNα treatment could induce cleavage/activation of ROCK1/2, in vivo. For these studies, we used a conditional Jak2V617F knock-in (KI) MPN mouse model30 (Fig. 5a). As expected, 5 weeks after transplantation of Jak2V617F KI bone marrow cells collected from Jak2V617F/+VavCre+ CD45.2 donor mice, a robust PV-like MPN phenotype developed in CD45.1 recipient mice (Supplementary Fig. 6a–f). Murine PEG-IFNα treatment was then initiated once a week for 4 weeks (Fig. 5a). As seen in previous MPN mouse model studies using IFNα31,32,33, PEG-IFNα treatment significantly reduced hematocrit (HCT) and red blood cell (RBC) levels in these mice (Supplementary Fig. 6g–j). Notably, PEG-IFNα treatment increased the cleavage of both ROCK1 and ROCK2 proteins in bone marrow mononuclear cells isolated from CD45.1 recipient mice (Fig. 5b–e). Additionally, we provide evidence that IFNα treatment induces activation/cleavage of caspase 3, PARP and ROCK proteins in both JAK2V617F-positive HEL cells and in JAK2V617F-negative U937 and KT-1 cells, in vitro, and these effects are repressed by co-treatment with a pan-caspase inhibitor, Z-VAD-FMK (Fig. 5f–h). In further studies, to determine whether PEG-IFNα treatment induces activation/cleavage of caspase 3 and activation of ROCK proteins in both Jak2+/+ (wild-type) and Jak2V617F/+ hematopoietic cells in vivo, we transplanted CD45.1 recipient mice with either Jak2+/+ or Jak2V617F/+ KI bone marrow cells collected from Jak2+/+VavCre- and Jak2V617F/+VavCre+ CD45.2 donor mice, respectively (Fig. 6a). Three weeks after transplantation, engraftment of Jak2+/+ and Jak2V617F/+ CD45.2+ cells in CD45.1 recipient mice was confirmed (Supplementary Fig. 7a) and a PV-like MPN phenotype developed in Jak2V617F/+, but not in Jak2+/+, recipient mice (Supplementary Fig. 7b–e). Murine PEG-IFNα treatment was then initiated once a week for 4 weeks (Fig. 6a). At week 3, 24 h post-IFNα treatment we collected peripheral blood and isolated mononuclear cells from the recipient mice (Fig. 6a, p-MYPT1 in peripheral blood mononuclear cells (PBMCs)). In both Jak2+/+ and Jak2V617F/+ recipient mice, PEG-IFNα treatment increased phosphorylation of the ROCK1/2 downstream target myosin phosphatase target subunit 1 (MYPT1)28, compared to vehicle-control-treated mice (Fig. 6b), consistent with an IFNα-induced increase in ROCK1/2 kinase activity. Importantly, IFNα-induced phosphorylation of p-MYPT1 was greater in Jak2V617F/+ compared to Jak2+/+ recipient mice (p = 0.0382). Additionally, PEG-IFNα treatment decreased hematocrit and red blood cell levels in Jak2V617F/+, but not in Jak2+/+, recipient mice (Fig. 6c, d and Supplementary Fig. 7f, g), consistent with earlier reports that IFNα treatment targets JAK2V617F-mutant over non-malignant hematopoietic cells32. Twenty-four hours after the fourth dose of PEG-IFNα, mononuclear bone marrow cells from recipient mice were isolated and we evaluated cleavage/activation of caspase 3 by immunoblotting and phosphorylation of MYPT1 by flow cytometry analyses. The data show that PEG-IFNα treatment induces cleavage of caspase 3 (Fig. 6e) and phosphorylation of MYPT1 (Fig. 6f, g) in both Jak2+/+ and Jak2V617F/+ bone marrow cells. These results were consistent with the analyses performed using bone marrow cells isolated from PEG-IFNα-treated wild-type C57BL/6 J mice (Supplementary Fig. 8). Together these results suggest that IFNα treatment induces caspase-dependent ROCK1/2 activation in normal and malignant hematopoietic cells, suggesting a potential role for ROCK1/2 in regulation of IFN-mediated biological responses.
Link to Figure 5: nature.com/articles/s41467-...
Link to Figure 6: nature.com/articles/s41467-...
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