Exogenous IFN-I administration promotes the enrichment and de novo induction of putative CSCs.
To investigate the impact of the IFN-I→IFNAR axis on the appearance of cancer cells with a stem-like phenotype (hereafter referred to as CSCs), we selected a panel of cancer cell lines of distinct origin (epithelial or mesenchymal) and species (human or mouse) and treated them for 72h with IFNs-I before assessing, by flow cytometry, the levels of prominin 1 (Prom1, best known as CD133), CD24 and CD44 surface markers, whose expression, alone and in combination, has been associated with putative CSCs. We observed that IFN-I exposure favors the enrichment of rare, CD133+CD24+CD44+ putative CSCs in all analyzed murine cancer cell lines. Specifically, we identified two main populations of IFN-I-enriched CSCs (IFN-CSCs) in MCA205 sarcoma cells: the CD133+CD24+CD44+low (CD44L) and the CD133+CD24+CD44+high (CD44H) CSC subsets (Figure 1a). Putative IFN-CSC fractions were also detected in AT3 breast carcinoma (BC), namely the CD133+CD44+CD24+low (CD24L) and CD133+CD44+CD24+high (CD24H) CSC subsets, whereby we focused exclusively on the former, the widely recognized CSC subpopulation in BC27 (Figure 1a). Similarly, we found (i) CD133+CD44+CD24+ in CT26 colon carcinoma cell line and (ii) CD133+CD44+CD24+low and CD133+CD44+CD24+high in B16.F10 melanoma cell line (Supplementay Figure 1a). These results are in line with the intra- and inter-tumoral heterogeneity often ascribed to CSCs28. To assess whether this phenomenon was exclusive of the murine cancer model, we treated human U2OS osteosarcoma and MDA-MB-231 BC cell lines with recombinant human IFN-α2a and then analyzed the expression of standard human CSC markers. As expected, we detected IFN-CSC subpopulations in both U2OS (CD133+CD44+ and CD44v6+CD24+ cell subsets) and MDA-MB-231 (CD133+CD44+ and CD44v6+CD24+low cell subsets) cell lines (Supplementary Figure 1b).
We then investigated whether IFN-CSC enrichment relied on the positive selection of pre-existing CSCs or on an active de novo induction of CSCs, a strategy cancer cells might deploy to evolve resistance. To address this question, we isolated MCA205 CD133+ and CD133- (i.e., non-CSC) cell fractions by fluorescence-activated cell sorting (FACS) and treated them with IFNs-I. Intriguingly, by flow cytometry, we found that IFN-I treatment led to a significant increase in the fraction of CD44H cells and the levels of the pluripotency transcription factor (TF) SRY (sex determining region Y)-box 2 (SOX2) in both the CD133+ and CD133- subsets (Figure 1b). In parallel quantitative RT-PCR (qRT-PCR) analyses of common stem-related TFs and CSC markers, we found that exogenous IFNs-I significantly upregulate Kruppel-like factor 4 (Klf4), POU domain, class 5, transcription factor 1 (Pou5f1, best known as Oct3/4), Sox2 and nestin (Nes) in FACS-isolated CD133- cells and Nanog homeobox (Nanog) in FACS-isolated CD133- and CD133+ cells (Figure 1b). These results suggest the co-occurrence of a process of positive selection of rare, pre-existing CSCs along with de novo CSC induction in response to exogenous IFNs-I.
We further analyzed the phenotypic and transcriptional profiles of IFN-CSCs, observing that IFN-I-treated epithelial cancer cells (AT3 and B16.F10) acquired a typical stem-like elongated morphology (Supplementary Figure 1c). Moreover, in distinct murine cancer cells, IFNs-I promoted the emergence of the side population (SP, a bona fide CSC feature), which was significantly reduced by co-treatment with verapamil (VRP), a blocker of ATP-binding cassette (ABC) transporters (Figure 1c and Supplementary Figure 1d). Finally, IFN-I exposure induced significant upregulation of Klf4, Oct3/4, Sox2, Nanog, hes family bHLH transcription factor 1 (Hes1) and Nes (Figure 1d and Supplementary Figure 1e), and endowed MCA205 and AT3 cancer cells with increased sphere forming ability (Figure 1e). Notably, only spheres pre-exposed to IFNs-I retained a CSC-related phenotypical and transcriptional profile when serially plated in standard CSC culture conditions (Figure 1f).
These data collectively demonstrate that exogenous IFNs-I favor the appearance of putative CSCs in multiple murine and human cancer cell lines.
IFN-I signaling, during immunogenic chemotherapy, triggers cancer cell stemness.
Since we have previously shown a key role for IFNs-I during bona fide ICD18, we asked whether CSC subpopulations could also be enriched during immunogenic chemotherapy. We took advantage of a library of pre-validated MCA-derived clones deficient for cardinal elements of the IFN-I pathway, including: (1) Ifnar1, (2) stimulator of interferon response cGAMP interactor 1 (Sting1, best known as Sting), (3) toll-like receptor 3 (Tlr3), (4) toll-like receptor adaptor molecule 1 (Ticam1, best known as Trif), (5) interferon induced with helicase C domain 1 (Ifih1, best known as Mda5), and (6) mitochondrial antiviral-signaling protein (Mavs, also known as Ips-1) (Figure 2a)18. We exposed these clones to the ICD inducer OXP (“donor” dying cells), then co-cultured “donor” dying cells with untreated clones of the same genotype (“receiving” viable cells) for 24h, and finally analyzed “receiving” cells at phenotypic and transcriptional levels (Supplementary Figure 2a). Similar to what observed upon IFN-I treatment, wild-type (Wt) clones responding to OXP displayed a significant increase of the two CD44H and CD44L CSC subpopulations (Figure 2b), which we will refer to as “ICD-CSCs”. Notably, ICD-CSC enrichment was impaired only in Ifnar-/- clones, indicating dependence on IFN-I signaling (Figure 2b). Consistently, both IFN-I and OXP treatment induced the accumulation of CSC-related transcripts in Wt clones and (even if to a lesser and heterogeneous extent) in Sting1-/-, Tlr3-/-, Ticam1-/-, Ifih1-/- and Mavs-/- clones, yet failing in Ifnar-/- clones (Figure 2c). Similarly, the ICD inducer DOX favored a complete transcriptional rewiring toward pluripotency by enhancing the expression of the entire panel of reprogramming factors analyzed, while the non-ICD drug cisplatin (CDDP), which we previously shown to induce very low levels of IFNs18, affected the expression of only few transcriptional factors (Figure 2d). OXP also promoted the appearance of a SP in all murine cancer cell lines (Figure 2e and Supplementary Figure 2b). Moreover, by exploiting DOX red fluorescence, we observed two distinct cell subsets (DOX+low and DOX+high) in DOX-treated MCA205 cells, differing in their capability to extrude DOX as well as Hoechst 33342 (Figure 2f and Supplementary Figure 2c). Notably, following drug withdrawal, only DOX+low cells survived and resisted re-challenge with diverse ICD inducers (Supplementary Figure 2d), indicating their multidrug tolerance/resistance29. To explore the in vivo appearance of ICD-CSCs, we locally treated MCA205 tumors growing in syngeneic immunocompetent mice with DOX or CDDP and evaluated CSC enrichment in recollected xenografts 15 days post-treatment (i.e., when tumors start escaping growth control18). Strikingly, we found a twofold increase of CD44H and NANOG+, upon DOX but not CDDP administration (Figure 2g).
Altogether, these results demonstrate that IFNs-I, during immunogenic chemotherapy, promotes CSC enrichment, both in vitro and in vivo, and point to this effect as an adaptive response cancer cells may deploy to escape therapy control.
Horizontal transfer of nucleic acids from dying to viable cancer cells, upstream of IFN-I signaling, drives cancer stemness.
To dissect the molecular mechanisms underlying ICD-CSC enrichment, we co-cultured OXP-treated “donor” MCA205 cells with untreated “receiving” MCA205 cells alone or in combination with benzonase (BNZase), which degrades all nucleic acids, or RNase A, RNase H or DNase, which selectively degrade ssRNAs, dsRNAs or DNA. We observed differential effects in the two CD44H and CD44L ICD-CSC subsets, with BNZase preventing the enrichment of both CSC populations, while RNase A, RNase H and DNase significantly affecting only CD44L cells (Figure 3a). Accordingly, BNZase halved the proportion of ICD-CSCs in “receiving” AT3 and CT26 cells (Supplementary Figure 3a). The observation that only the depletion of all nucleic acids nullifies the enrichment of ICD-CSCs, again suggests that this phenomenon depends on an intact IFN-I signaling.
We next investigated the involvement of extracellular vesicles (EVs) in ICD-CSC enrichment. EVs isolated from “donor” MCA205 cells and stained with the non-toxic fluorescent membrane dye PKH26 were added to “receiving” MCA205 cells (Supplementary Figure 3b). EV uptake in “receiving” cells, confirmed by fluorescence microscopy and flow cytometry (Figure 3b), induced a significant increase of CD44H and CD44L CSC percentages and of the expression of most reprogramming factors, which were prevented by co-treatment with the actin inhibitor cytochalasin D (cyto D) (Figure 3c,d). Intriguingly, EVs from OXP-treated cancer cells carried mRNAs for reprogramming factors (Klf4, Myc, Oct3/4, Sox2, Nanog, Hes1, Nes), invasion molecules [snail family zinc finger 1 (Sna1, best known as Snail), Twist-related protein 1 (Twist1, also known as bHLHa38), Cadherin-2 (Cdh2, also known as N-cadherin/Ncad), Vimentin (Vim), and Fibronectin (Fn1)] and ICs, [Pdl1, programmed cell death 1 ligand 2 (Pdcd1lg2, also known as Pdl2), and lectin, galactose binding, soluble 9 (Lgals9, best known as galectin-9) Figure 3e], suggesting their contribution to cancer cell de-differentiation and aggressiveness during immunogenic chemotherapy.
Altogether, these data indicate that ICD-CSC enrichment occurs through paracrine processes involving free and EV-mediated transfer of nucleic acids and stem-related mRNAs.
IFN-CSCs and ICD-CSCs exhibit heterogeneity of drug-response, tumorigenic and invasive potential, and immunogenicity.
We then analysed FACS-isolated CD44H and CD44L ICD-CSCs separately, and searched for hallmark CSC features like chemo-refractoriness, self-renewal ability, tumorigenic and metastatic potential, and the capability to escape immune control. We treated CD44H and CD44L cells with various ICD inducers, and found a diverse sensitivity to drugs, with only CD44H cells showing a higher therapeutic resistance than parental counterparts, both in vitro (Supplementary Figure 4a) and in vivo (Figure 4a), upon transplantation in immunocompetent mice. On the one hand, by monitoring the in vitro evolution of FACS-isolated MCA205 ICD-CSCs, we demonstrated as both subsets were able to rapidly regenerate the phenotypic complexity of parental cells (Figure 4b). On the other hand, in vivo studies revealed that CD44H ICD-CSCs are significantly more tumorigenic and less immunogenic than CD44L ICD-CSCs. Indeed, although both subpopulations were able to generate tumors in immunocompromised NOD SCID gamma (NSG) mice, only CD44H ICD-CSCs developed neoplasms at the lowest doses and overcame immunosurveillance thus growing in immunocompetent hosts at the highest number of injected cells (Figure 4c). Consistently, only half of the immunocompetent mice rejecting CD44H ICD-CSCs were vaccinated against viable parental cells (Figure 4d). Conversely, CD44L ICD-CSCs or parental MCA205 cells endowed animals with 100% long-term protection against tumor re-challenge. Moreover, when intravenously injected into immunocompetent mice, CD44H (but not CD44L) ICD-CSCs developed lung metastases (Figure 4e).
Since we identified CD44H ICD-CSCs as the MCA205 subpopulation mainly driving in vivo tumor aggressiveness and therapeutic resistance, we focused on this subset. To gain insights into the immunogenicity of ICD-CSCs, we analyzed the proliferation rate of isolated CD8+ H-2Kb/ovalbumin (OVA)-specific OT-1 T cells previously primed with dendritic cells (DCs) that had taken up apoptotic OVA-expressing CD44H (CD44H-OVA) ICD-CSCs or parental cells, and then boosted with viable cells of the same type. In line with the immune privileged nature observed in vivo (Figure 4c,d), CD44H-OVA ICD-CSCs induced a significantly lower expansion of OT-1 CD8 T cells than parental conterparts (Figure 5a) and resisted CD8-mediated killing (Figure 5b). These data prompted us to hypothesize that CD44H ICD-CSCs could escape immune control by inducing CD8 T cell exhaustion. To pursue this hypothesis, we analyzed the expression of common IC ligands, finding the upregulation of PDL1, PDCD1LG2, CEA1 and LGALS9 (Figure 5c). Consistently, CD8+ T tumor-infiltrating lymphocytes (TILs) isolated from MCA205-bearing mice 15 days after intratumoral injection of DOX (when CSC enrichment occurs), but not of CDDP (which does not enrich for CSCs), displayed a significant upregulation of the LGALS9 receptor IC Hepatitis A virus cellular receptor 2 (HAVCR2, best known as TIM-3) (Figure 5d). We extended the characterization of ICD-CSCs to AT3 cells (i.e., the CD24L cell subset), and confirmed their regenerative potential (Supplementary Figure 4b) as well as the downregulation of the histocompatibility 2, K1 (H2-K1), and the upregulation of the IC ligands PDL1, PDCD1LG2 and LGALS9 (Figure 5c) and of the invasiveness markers Snail, Twist1, Ncad and Fn1 (Supplementary Figure 4c).
To further characterize ICD-CSC immunogenicity, we measured cytokine production through Luminex Multiplex Assay, observing a unique chemokine secretion pattern in CD44H MCA205 and CD24L AT3 ICD-CSCs as compared to their respective parental cells. This encompasses reduced levels of proinflammatory chemokines CCL2 and CCL5, which mediate inflammatory monocyte trafficking and DC-T cell interactions30, and enhanced capability to secrete CXCL1 and CXCL2 (the latter in CD24L AT3 cells), which promote chemoresistance and metastasis31 (Figure 5e). Notably, CD24L AT3 cells also showed higher levels of the regulatory T cell chemoattractant CCL2232 than parental AT3 cells. Accordingly, when CD24L ICD-CSCs or parental AT3 cells were confronted with histocompatible splenocytes in ad hoc microfluidic devices33 and then analyzed by videomicroscopy for their in vitro capability to recruit immune cells, only parental cells were able to attract and stably interact with splenocytes at as early as 24h (Figure 5f,g and Supplementary Movies 1-4). On the contrary, CD24L ICD-CSCs failed to do so and, instead, migrated towards splenocytes starting a fleeting and unproductive interaction only upon 48h. Finally, when we confronted parental and CD24L AT3 cells in a microfluidic “competition” device (Supplementary Figure 4d), immune cells selectively migrated towards parental cells, moving away from CSCs (Figure 5h,i).
Altogether, these results allowed us to make several key observations: adaptation of cancer cells to immunogenic chemotherapy enables cell selection and drives phenotype switching. Both phenomena actively contribute to intratumor heterogeneity as the collection of CSC subpopulations have differential therapeutic response, aggressiveness and immunogenicity.
Global chromatin remodeling downstream of IFNs-I.
To dissect the mechanisms underlying cancer cell reprogramming downstream of IFNs-I, we mapped the chromatin landscape of parental (P) and CD44H (H) MCA205 cells by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) (Figure 6a-c). By analyzing ATAC-seq peaks, we conceived a closed-to-open (C→O) and an open-to-closed (O→C) logic, and stratified genes in 4 groups. The CPCH and OPOH groups comprise genes with peaks permanently closed (i.e., putatively repressed) or open (i.e., putatively expressed) in both samples, while the CPOH and OPCH groups comprise genes whose peaks are closed in parental cells and open in CD44H IFN-CSCs and viceversa. In particular, we focused on the CPOH group containing genes putatively more expressed in CSCs. Intriguingly, this group encompasses genes involved in cancer stemness (Myc and Sox), embryonic development (Tbx4), epithelial-to-mesenchymal transition (EMT) (Gata6 and Tfcp2), cancer cell invasiveness and metastatization (Myct1, Spire1 and Trpm4), tumorigenesis, tumor progression and therapy resistance (Slc6a6, Baiap2, Ttll7 and Wee1), the negative regulator of the antigen presentation machinery (APM) Gpr17, and the inhibitor of granzyme activity Serpin (Figure 6a). Consistently, in the OPCH group we found tumor suppressor genes (Cdh, Cdk2ap1, Dlg2, Ripk3 and Fbxw2) and genes controlling tumor growth (Mtor and Ncam1), APM functionality (Tap1, Tap2 and Ctsl) and inflammation (Il24, Il27, Gsdmd and Uba7) (Figure 6a). Subsequent integration with RNA-seq analyses confirmed an increased expression of genes involved in tumorigenesis, tumor progression, invasiveness (e.g., Csf1r, Trpm4, Itga5, Wee1, Baiap2, Ttll7 and Spire1) and immune escape (e.g., Gpr17), coupled with repression of genes involved in tumor suppression and immune recognition (like Cdh1, Il12b, Tlr5, Cdk2ap1, Il34, Il16 and Ctsl) in CD44H IFN-CSCs, as compared to parental cells (Figure 6d).
We next inferred and reconstructed protein–protein interaction subnetworks and biological processes specifically modulated in CD44H IFN-CSCs by using the clusterProfiler and enrichPlot R packages (Figure 6e and Supplementary Figure 5a). Gene ontology (GO) analysis showed that most of the upregulated genes in CD44H cells (red module) have significant functional connections with cell growth promotion, stemness maintenance and tissue remodeling, with immune suppression (e.g., negative regulation of leukocyte activation), despite an intact response to IFN-I and IFN-II, with response to stress (e.g., positive regulation of response to DNA damage stimulus, regulation of autophagy and apoptosis), lipid metabolism, and, of note, with enhanced chromatin accessibility. Accordingly, we organized the downregulated genes (blue module) into 4 biological processes: cell growth arrest, cell differentiation, oxidative phosphorylation and protein dephosphorylation. These results provide clues about the modular re-organization of specific pathways downstream of IFNs-I.
Of note, among the genes specific of the CSC fraction (CD44H cells), we also identified multiple ISGs, including (but not limited to) Ifi27l2a, Ifi27l2b and the epigenetic regulator Kdm1b (Figure 6a,b). We were particularly intrigued by Kdm1b since chromatin remodeling plays a critical role in cancer evolution, cellular plasticity and immune escape12, 34, 35, 36. At first, we measured the enrichment of TF-binding motifs in the ATAC-seq study by using the HOMER motif software (Figure 6c and Supplementary Figure 5b). We observed significant differences between CSCs and parental cells, in particular we found enrichment of motifs for various TFs of the helix-turn-helix (HTH) superfamily (i.e., RFX, Rfx1, Rfx2, Rfx5 and X-box), the Homeobox basic helix-loop-helix (bHLH) member Pitx1:Ebox, the Rel homology domain (RHD) family member NFkB-p65, and the zinc finger (Zf) family member ZBTB in CD44H cells, suggesting their major role in the global chromatin remodeling in CSCs. Conversely, the Zf motifs CTCF, BORIS and NRSF, the transcriptional enhanced associate domain (TEA, TEAD) motifs (i.e., TEAD and TEAD1-4), the Rel homology domain (RHD)-basic leucine-zipper (bZIP) superfamily member NFAT-AP1, the ETS, RUNT, the interferon-sensitive response element (ISRE) and the CCAAT box-binding transcription factor (CTF) motifs were more accessible in parental cells. Thereafter, we explored the role of the ISG KDM1B in the induction of ICD-CSCs. To this aim, we added the KDM1B inhibitor tranylcypromine (TCP) to the “donor”-“receiving” in vitro co-culture and found a significant reduction of CD44H percentages in “receiving” cells (Figure 6f). Of note, in vivo administration of TCP in MCA205 tumor bearing mice (Figure 6g, left panel), prevented the enrichment of ICD-CSCs as well as the induced expression of TIM-3 on CD8+ TILs (Figure 6g, central and right panels).
Overall, these data demonstrate that KDM1B, downstream of IFNs-I, edits the epigenome of cancer cells toward stemness, immune escape and therapy resistance (Figure 6h).
IFN-I metagenes correlate with stemness in BC patients.
To investigate the clinical relevance of the IFN-I→KDM1B axis, we first calculated the Spearman correlation between KDM1B, IFN-I-related metagenes, stem-related reprogramming factors and IC ligands in multiple publicly available transcriptomic data of BC patients responsive to anthracyclines18, 37. We observed that the expression levels of KDM1B significantly correlated with those of MYC and POU5F1 in two out of three available datasets and of IFNB1, CXCL10, and CD274/PD-L1 in at least one dataset (Figure 7a). Along similar lines, IFNB1 expression positively correlated with the expression of SOX2 in half of the analyzed datasets, of KLF4, NES and PDCD1LG2/PD-L2 in one dataset, and of POU5F1 and NANOG in two datasets (Figure 7a and Supplementary Figure 6a). Similarly, the ISGs MX1, CXCL10, DHX58, OASL and STAT1 correlated with the stemness factors MYC, POU5F1, SOX2 and NANOG, and with the IC ligands PDCD1LG2/PD-L2 and CD274/PD-L1, these last in turn correlating with KLF4, MYC, POU5F1, SOX2 and NANOG, in at least one dataset (Figure 7a and Supplementary Figure 6a). Next, we selected a BC cohort including 1902 patients on the online biomarker validation tool Metabric (Figure 7b,c and Supplementary Figure 6b-e) and performed multivariate survival analysis by stratifying patients into two groups, according to risk behavior. In details, patients were assigned to either the high-risk or the low-risk group based on the high and low expression, respectively, of gene pairs selected among KDM1B-related, IFN-I-related and stem-related factors (KDM1B-SOX2, MX1-SOX2, CXCL10-SOX2, and OASL-SOX2). Of note, high-risk group patients exhibited a significantly reduced distant and local recurrence-free incidences (Figure 7b and Supplementary Figure 6b-d) and, accordingly, disease-specific survival was decreased if compared to low-risk group patients (Figure 7c and Supplementary Figure 6e).
To further correlate IFN-I and CSC signatures, we performed longitudinal immunohistochemistry (IHC) analyses on consecutive formalin fixed paraffin-embedded BC biopsies, assessing the expression of MX1 and CD44-CD24 on CD45- cancer cells at pre- (T0; at diagnosis) and post- (T1, at surgery) neo-adjuvant anthracycline-based chemotherapy (Figure 7d-f and Supplementary Table 1). We found a significant increase of CD44+CD24-/+low Allred scores in 15% of cases (Figure 7f). Altogether, these results suggest the co-occurrence of IFN-I signature and CSC markers during anthracycline-based immunogenic chemotherapy.