Absence of NKG2D ligands defines leukaemia stem cells and mediates their immune evasion

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Abstract

Patients with acute myeloid leukaemia (AML) often achieve remission after therapy, but subsequently die of relapse1 that is driven by chemotherapy-resistant leukaemic stem cells (LSCs)2,3. LSCs are defined by their capacity to initiate leukaemia in immunocompromised mice4. However, this precludes analyses of their interaction with lymphocytes as components of anti-tumour immunity5, which LSCs must escape to induce cancer. Here we demonstrate that stemness and immune evasion are closely intertwined in AML. Using xenografts of human AML as well as syngeneic mouse models of leukaemia, we show that ligands of the danger detector NKG2D—a critical mediator of anti-tumour immunity by cytotoxic lymphocytes, such as NK cells6,7,8,9—are generally expressed on bulk AML cells but not on LSCs. AML cells with LSC properties can be isolated by their lack of expression of NKG2D ligands (NKG2DLs) in both CD34-expressing and non-CD34-expressing cases of AML. AML cells that express NKG2DLs are cleared by NK cells, whereas NKG2DL-negative leukaemic cells isolated from the same individual escape cell killing by NK cells. These NKG2DL-negative AML cells show an immature morphology, display molecular and functional stemness characteristics, and can initiate serially re-transplantable leukaemia and survive chemotherapy in patient-derived xenotransplant models. Mechanistically, poly-ADP-ribose polymerase 1 (PARP1) represses expression of NKG2DLs. Genetic or pharmacologic inhibition of PARP1 induces NKG2DLs on the LSC surface but not on healthy or pre-leukaemic cells. Treatment with PARP1 inhibitors, followed by transfer of polyclonal NK cells, suppresses leukaemogenesis in patient-derived xenotransplant models. In summary, our data link the LSC concept to immune escape and provide a strong rationale for targeting therapy-resistant LSCs by PARP1 inhibition, which renders them amenable to control by NK cells in vivo.

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Fig. 1: Absence of immunostimulatory NKG2DLs identifies chemotherapy-resistant LSCs.
Fig. 2: NK cells preferentially lyse non-LSCs.
Fig. 3: Absence of NKG2DLs identifies LSCs in both non-CD34-expressing and CD34-expressing cases of AML.
Fig. 4: PARP1 expression represses NKG2DLs in LSCs and contributes to their selective escape from immune surveillance by NK cells.

Data availability

All data generated are included in the published Letter and in its Supplementary Information. Gene-expression data that support the findings of this study have been deposited in the Gene Expression Omnibus under accession numbers GSE127200 and 127959. All data are also available from the corresponding author on reasonable request.

Change history

  • 01 August 2019

    An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Acknowledgements

This study was supported by grants from the Deutsche Forschungsgemeinschaft (LE 2483/7-1 to C.L.; SA1360/9-1, SA1360/7-3 to H.R.S.; and SFB873, FOR2674 and FOR2033 to A.T.), the Swiss National Science Foundation (179239) and the Foundation for Fight Against Cancer (Zürich) to C.L., Germany’s Excellence Strategy (EXC 2180/1), the Wilhelm Sander-Stiftung (2007.115.3 to H.R.S. and 2019.042.1 to C.L.), the Deutsche Krebshilfe (111828, 70112914) to H.R.S., the SyTASC consortium (Deutsche Krebshilfe), the Swiss Bridge Foundation and the Dietmar Hopp Foundation to A.T. We thank Amgen for the NKG2D antibody clone 6H7; U. Kohlhofer, A. Jauch, M. M. Martinez and Z. Gu for experimental assistance; and the Animal and Flow Cytometry Facilities in Basel, Heidelberg, Tübingen and the Genomics & Proteomics Core Facility (DKFZ) for support.

Reviewer information

Nature thanks Ross Levine and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Author information

A.M.P., K.R., S.R., M.K. and J. Steinbacher designed and performed experiments, analysed data and generated figures and tables. A.M.P. performed mouse studies, flow cytometry, expression of NKG2DLs, sorting, in vitro treatments, colony and apoptosis assays, qRT–PCR and cord blood samples; K.R. performed expression of NKG2DLs, sorting, pNKC generation, in vitro NK cell and colony-forming unit assays, AML samples and biometric analysis, and contributed to mouse experiments; S.R. performed patient-derived xenotransplant models, RNA sequencing and figures on bioinformatics data; M.K. performed expression of NKG2DLs, sorting, in vitro treatments, colony-forming unit assays, gene-expression arrays, qRT-PCR and bioinformatic analysis; J. Steinbacher performed AML samples, expression of NKG2DLs and in vitro NK cell and colony-forming unit assays. H.W., C.T., M.M., P.H., T.S., M.F., E.N., P.L., L.Q.-M. and S.D. performed experiments and analysed the resulting data. H.W. performed immunoblots, chromatin immunoprecipitation and qRT–PCR. C.T. performed expression of NKG2DLs, in vitro NK cell assays and AML samples. M.M. and P.H. performed mouse assays and cord blood samples. T.S. performed immunoblots. M.F. performed bioinformatic analyses. E.N. performed PARP inhibition in healthy mice. P.L. performed next-generation sequencing and qRT–PCR. L.Q.-M. and S.D. performed mouse histopathology. L.K. and D.D. took patient samples and clinical data. J.R.P. interpreted data. C. Lutz, J. Schwaller, R.Z., B.R.B. and M.A.C. provided critical reagents. C. Lutz provided AML cells. J. Schwaller, R.Z., B.R.B. and M.A.C. provided mouse leukaemia cells. A.S. provided NKG2DL reagents and contribution to experimental design. A.T. contributed to the study design, performed data analysis, wrote the manuscript and supervised the study. H.R.S. conceived the study, analysed data, wrote the manuscript and supervised the study. C. Lengerke conceived the study, analysed the data, and supervised the study and wrote the manuscript as lead author. All authors critically reviewed the manuscript.

Correspondence to Helmut R. Salih.

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Extended data figures and tables

Extended Data Fig. 1 Surface expression of NKG2DLs and associated features of cell morphology, clonogenicity and gene expression.

a, Human AML cells show heterogeneous surface expression of the NKG2D ligands MICA, MICB, ULBP1 and ULBP2, ULBP5 or ULBP6. Flow cytometry analysis with antibodies against human MICA, MICB, ULBP1 or ULBP2, ULBP5 or ULBP6 in primary AML samples from n = 62 patients. be, Surface expression of NKG2DLs distinguishes leukaemic subpopulations with different morphology, clonogenic capacity and molecular characteristics. AML cells stained with conjugated NKG2D–Fc chimeric protein were sorted according to expression of NKG2DLs and analysed by May–Grünwald–Giemsa stainings (b) and forward and sideward flow cytometry plots (c). When compared to corresponding NKG2DL (NKG2DLneg) AML cells isolated from the same patient, NKG2DL+ (NKG2DLpos) AML subpopulations display more-mature morphology, irrespective of CD34 expression. d, Furthermore, colony-forming assays indicate intermediate clonogenicity in AML cells with intermediate surface expression of NKG2DLs (NKG2DLinterm AML cells; left, representative plot depicting sorting strategy, no. 37; right, summarized results from technical triplicate analyses performed with n = 3 cases of AML). Centre values represent mean, error bars represent s.d.; one-way ANOVA was used for statistical analysis. e, GSEA analyses reveal enriched haematopoietic stem cell and suppressed progenitor signatures in NKG2DL compared to NKG2DL+ AML cells (no. 1, 6, 7, 8 and 12). Source Data

Extended Data Fig. 2 Only NKG2DL subpopulations of AML cells are serially re-transplantable and selectively engraft NSG mice after intrafemoral injection.

ac, Bone marrow cells isolated from mice transplanted with NKG2DL AML cells were re-transplanted into sublethally irradiated secondary recipient mice, either unsorted (a, n = 7 cases of AML) or after sorting into NKG2DL and NKG2DL+ AML cells (b, c, no. 1) (see Supplementary Table 2). Flow cytometric analyses in secondary recipients are shown, indicating percentages of engrafted human AML cells among total bone marrow cells at 12 (a) or 15 (b) weeks after transplantation. Each dot represents one transplanted mouse; n = 2 mice for NKG2DL; n = 3 mice for NKG2DL+. c, Histological analyses of mice (H&E and anti-CD33 show exemplary data, no. 1; two analysed mice for NKG2DL and three for NKG2DL+ cells). The NKG2DL staining procedures do not affect the results. d, NKG2DL and corresponding NKG2DL+ cells were sorted either using NKG2D–Fc (n = 65 mice for NKG2DL; n = 79 mice for NKG2DL+; n = 12 cases of AML) or using pooled antibodies against individual NKG2DLs (MICA, MICB, ULBP1 and ULBP2, ULBP5 or ULBP6; n = 3 cases of AML; n = 8 mice per group) and then transplanted at equal numbers for each case of AML intrafemorally in pre-irradiated NSG mice. For detailed mouse numbers per patient and subpopulation, see Supplementary Table 2. Human leukaemic engraftment in mouse bone marrow was assessed 12–16 weeks after transplantation; percentages are shown of human leukaemic among mouse bone marrow cells in mice transplanted with NKG2DL or NKG2DL+ subpopulations for each case of AML. Centre values represent means; each dot represents one mouse; a Student’s t-test was used for statistical analysis. Note that these samples are also included in the summarized analysis shown in Fig. 1g. e, AML cells with variable expression of NKG2DLs were stained with NKG2D–Fc, isotype or empty control and analysed side-by-side without prior sorting. f, Quantifications of results obtained in colony formation (left), homing (middle) (n = 3 mice per group and patient sample, except for n = 4 mice in NKG2D–Fc-stained group with patients no. 13 and 76) and in vivo long-term engraftment assays in NSG mice (right). Mice per patient sample and condition: no. 110, 3 NKG2D–Fc, 3 isotype and 2 empty control; no. 76, 2 NKG2D–Fc, 2 isotype and 2 empty control; no. 13, 3 NKG2D–Fc, 3 isotype and 2 empty control; and no. 72, 4 NKG2D–Fc, 4 isotype and 3 empty control. g, Annexin V and 7-AAD stainings indicating apoptotic (left) and live (right) cells among AML cells incubated for 24 h with NKG2D–Fc, isotype or control medium (n = 10 cases of AML). f, Two-sided Kruskal–Wallis test was used for statistical analysis. Centre values represent mean, error bars represent s.d. Source Data

Extended Data Fig. 3 Association between surface expression of NKG2DLs and molecular and clinical parameters in patients with AML.

a, Cells from patients with known genetic and molecular profiles were stained with conjugated NKG2D–Fc chimeric protein and included in the analyses. Numbers of patients with positive or negative results for the respective mutation are shown below each analysis; patients with an unknown result for the particular analysis are not shown. Note that cases of AML that belong to the favourable molecular European LeukaemiaNet (ELN) risk group or with detectable inv(16) showed higher expression of NKG2DLs when compared to AML of other risk groups or without inv(16). For statistical analyses, a Kruskal–Wallis test was used for karyotype and ELN 2017 risk group, and a Mann–Whitney U test for all other data. be, Surface expression of NKG2DLs assessed at diagnosis (b) was compared between patients who achieved or did not achieve complete remission (CR) or complete remission with incomplete haematologic recovery (CRi) after induction chemotherapy (c), as well as between those patients who—after achieving complete remission (both with and without incomplete haematologic recovery)—did or did not experience subsequent relapse (d). Patients with initial high percentages of NKG2DL+ cells among total AML cells more often achieve—and, by trend, also sustain—remission. A Mann–Whitney U test was used for statistical analysis. a, c, d, Boxes indicate the median and interquartile range, and whiskers represent data up to 1.5 × the interquartile range; outliers that range from 1.5–3 × the interquartile range are depicted as circles. In e, patients with high (n = 75) versus low (n = 75) expression of NKG2DLs (left), and patients with ≥80% NKG2DL+ (n = 24) versus ≥ 80% NKG2DL (n = 56) cells among total AML cells (right) were compared with respect to overall survival. Note that when only patients younger than 65 years are included, improved survival is observed in cases with ≥80% NKG2DL+ compared to ≥80% NKG2DL cells among total AML cells (as shown in Fig. 1p). For survival analyses, the log-rank (Mantel–Cox) test was used for statistical analyses. For all other tests, two-sided statistical tests were used.

Extended Data Fig. 4 Expression of NKG2DLs on mouse leukaemic cells and association with a lack of leukaemogenicity in syngeneic mouse models.

a, b, Staining of whole bone marrow cells derived from healthy wild-type (WT), pre-leukaemic (chromatin immunoprecipitation, Dnmt3a or Tet2 mutated) or leukaemic (Mll-Enl, Mll-ptd/Flt3-ITD and Mll-Af9) mice using a mouse NKG2D tetramer. Representative flow cytometric plots (a) and summarized quantifications of NKG2DL+ cells among total mouse bone marrow cells (b) (n = 3 mice per model and condition; a two-sided Student’s t-test was used for statistical analysis). cm, NKG2DL and corresponding NKG2DL+ cells were sorted from leukaemic Mll-Enl and Mll-ptd/Flt3-ITD mice and analysed by qRT–PCR for the genetic leukaemic driver (c) (Mll-Enl mice, n = 3), and at equal numbers in colony-forming assays (d) (n = 6 for Mll-Enl mice; n = 3 for Mll-ptd/Flt3-ITD mice). en, In vivo primary and secondary transplantation (tx) assays. e, j, Kaplan–Meier-survival analyses (n = 24 mice for primary transplantations; n = 18 mice for secondary transplantations; log-rank Mantel–Cox test was used for statistical analysis). f, k, Spleen assessment with representative images and weight quantification (fMll-Enl mice, primary transplantation, n = 9 NKG2DL and n = 12 NKG2DL+; secondary transplantation, n = 10 NKG2DL and n = 12 NKG2DL+; k, Mll-ptd/Flt3-ITD mice, primary transplantation, n = 15 NKG2DL and n = 13 NKG2DL+; secondary transplantation, n = 9 NKG2DL and n = 11 NKG2DL+). g, l, Peripheral blood counts (gMll-Enl mice, primary transplantation, n = 6 NKG2DL and n = 6 NKG2DL+; secondary transplantation, n = 10 NKG2DL and n = 9 NKG2DL+; lMll-ptd/Flt3-ITD mice, primary transplantation, n = 14 NKG2DL and n = 12 NKG2DL+; secondary transplantation, n = 11 NKG2DL and n = 11 NKG2DL+). RBCs, red blood cells; WBCs, white blood cells. h, m, i, n, Representative histopathological analyses: spleen (h, m), bone marrow (i, n). H&E. Scale bars, 50 μm. A two-sided Mann–Whitney U test (g, l, WBCs, primary transplantation; g, platelets, secondary transplantation) or a two-sided Student’s t-test (all other analyses) were used for statistical analysis. Centre values represent mean, error bars represent s.d. for all plots. Source Data

Extended Data Fig. 5 Leukaemogenicity of mouse NKG2DL and NKG2DL+ subpopulations after transplantation in syngeneic recipients depleted or not of endogenous NK cells.

Sorted NKG2DL and NKG2DL+ leukaemic cells isolated from Mll-Enl and Mll-ptd/Flt3-ITD genetic models were transplanted into syngeneic mice with or without in vivo depletion of NK cells (NKCD). Engraftment (Ly5.2 chimerism), leukaemia induction and survival were assessed in primary and secondary transplantation assays. a, e, Kaplan–Meier survival analyses. b, f, Quantification of spleen weights and representative spleen pictures. c, g, Peripheral blood counts. ah, Donor-derived Ly5.2 chimerism among Ly5.1 bone marrow recipient cells for Mll-Enl (ad) and Mll-ptd/Flt3-ITD (eh) cells. Exact numbers of mice transplanted and analysed for each genetic leukaemia model, subpopulation, condition and analysis type are indicated below. i, Representative flow cytometry plots showing successful NKCD by treatment with InvivoMab anti-Nk1.1 antibody (250 μg per mouse per week, first application 24 h before transplantation); a two-sided Student’s t-test and a log-rank Mantel–Cox test (for Kaplan–Meier survival analyses) were used for statistical analysis. Centre values represent mean, error bars represent s.d. for all plots. a, Primary transplantation, n = 11 NKG2DL, n = 12 NKG2DL+; secondary transplantation, n = 6 per group; b, primary transplantation, n = 3 NKG2DL, n = 6 NKG2DL+; secondary transplantation, n = 4 NKG2DL, n = 6 NKG2DL+; c, primary transplantation, n = 3 per group; secondary transplantation, n = 4 NKG2DL, n = 3 NKG2DL+; d, primary transplantation, n = 5 per group (for controls without NKCD, n = 8 mice per group); secondary transplantation, n = 6 per group; e, primary transplantation, n = 3 NKG2DL, n = 6 NKG2DL+; secondary transplantation, n = 4 NKG2DL, n = 6 NKG2DL+; f, primary transplantation, n = 6 per group; secondary transplantation, n = 3 NKG2DL, n = 5 NKG2DL+; g, primary transplantation, n = 6 NKG2DL, n = 6 NKG2DL+; secondary transplantation, n = 3 NKG2DL, n = 6 NKG2DL+; h, primary and secondary transplantation, n = 5 mice per group or, respectively, for controls without NKCD: primary transplantation, n = 7 per group; secondary transplantation, n = 8 for NKG2DL, n = 6 for NKG2DL+. Source Data

Extended Data Fig. 6 Differential recognition of NKG2DL+ versus NKG2DL and CD34+ and CD34 subpopulations of AML cells by NK cells, and effects of NK cell co-culture on leukaemogenic capacity and expression of immunomodulatory markers in human AML cells.

Leukaemic engraftment after pre-culture with NK cells and expression. a, Depletion of NKG2DL+ AML cells after in vitro co-culture with pNKCs. Flow cytometric quantification of NKG2DL+ AML cells (no. 10, 13, 15, 17, 35 and 36) after co-culture with pNKCs for 16 h at the indicated effector/target ratios. A Kruskal–Wallis test was used to test for statistical significance. bd, Differential recognition of CD34+ (LSC-enriched) versus CD34 (non-LSC) subpopulations of AML cells. pNKCs were cultured with sorted CD34+ or corresponding CD34 AML cells (one dot represents one patient sample, n = 7 cases of AML). Analyses of pNKC-mediated cytotoxicity (b), percentages of CD69+ and CD107a+ among total pNKCs (c) and IFNγ, perforin, granzyme B and TNF concentrations in supernatants (d). Two-sided unpaired t-tests (b, c), and Kruskal–Wallis tests (d) were used for statistical analyses. e, f, Leukaemic engraftment in mice transplanted with AML cells derived from in vitro cultures with or without NK cells. Mice transplanted with equal numbers of AML cells (n = 3 mice per condition and patient as indicated) derived from control cultures without NK cells and from anti-NKG2D + pNKC co-cultures did not show leukaemic repopulation in peripheral blood and bone marrow at time points at which engraftment was detected in mice transplanted with corresponding AML cells from mock + pNKC conditions (shown in Fig. 2e). As shown here, these mice engrafted later. Leukaemic burden as quantified by flow cytometry (e) at the delayed time points when leukaemia was detected in these control groups (f). The time points of engraftment of AML cells cultured with unblocked pNKCs (mock + pNKCs) are shown side-by-side to illustrate that, for each patient sample, this condition showed the fastest engraftment. A two-sided Student’s t-test was used for statistical analysis. gl, Expression of additional immunomodulatory molecules in LSCs compared to non-LSCs, before and after co-culture with NK cells. Analyses of surface expression of CD112, CD155 and B7-H6 (each in n = 23 cases of AML), CD80, CD86 and PD-L1 (each in n = 25 cases of AML), CD47 (n = 14 cases of AML), and HLA-ABC (n = 75 cases of AML) after co-staining of bulk AML cells for NKG2DLs (g), CD34 (h), CD155 (i) and CD112 (j) on NKG2DL and NKG2DL+ AML cells after co-culture with the indicated ratios of pNKCs compared to cultures without pNKCs (‘AML alone’), and indicated GSEA analyses of gene-expression datasets from sorted LSCs and non-LSCs isolated as indicated (k, no. 1, 6, 7, 8 and 12; l, no. 7, 8 and 12). Statistical analyses in gj were performed using a two-sided Mann–Whitney U test. Centre values represent mean, error bars represent s.d. (ae) or s.e.m. (gj). One dot represents one patient sanple (ad, gj) or one mouse (e). Nominal P value and normalized enrichment score (k, l). Source Data

Extended Data Fig. 7 Surface expression of NKG2DLs in non-CD34-expressing versus CD34-expressing AML, analysis of in vivo leukaemogenicity in CD34+ versus CD34 subpopulations of AML cells and co-staining for NKG2DL and LSC markers.

a, Comparison of expression of NKG2DLs (SFI, specific fluorescence intensity indices) as measured by NKG2D–Fc in non-CD34-expressing (n = 57, left) and CD34-expressing (n = 107, right) cases of AML. b, Characteristics of patients with >99% NKG2DL+ cells among AML cells within our cohort (comprising n = 175 cases of AML; note that all cases are non-CD34-expressing cases of AMLs. c, Quantification of individual patient data shown in a, and of expression of NKG2DLs in CD34+ versus CD34 subpopulations within CD34-expressing cases of AML for which individual data are shown in d. A two-sided Mann–Whitney test was used for statistical analysis. eh, Analysis of sorted CD34+ and CD34 subpopulations of AML cells in in vivo xenotransplantation assays in NSG mice (no. 7, 8 and 12; n = 5 mice per AML and subpopulation). e, f, Flow cytometric analysis of summarized percentages of human leukaemic among mouse bone marrow (e), and spleen and liver cells (f). g, Histopathological bone marrow analysis using antibodies that recognize human, but not mouse, CD33 and CD34; 630× magnification. h, Kaplan–Meier analysis indicating mouse survival. A Mann–Whitney U test was used for statistical analysis. Note that CD34+ subpopulations with lower percentages of NKG2DL+ cells have increased stemness properties. i, j, Analysis of the percentage of positive cells with MICA, MICB, ULBP1 or ULBP2, ULBP5 or ULBP6 surface expression in non-CD34-expressing cases of AML (n = 29) (i) and in CD34+ and CD34 subpopulations of CD34-expressing cases of AML (n = 33) (j). In some cases the sum of the percentage of positive cells exceeds 100%, which reflects the fact that individual AML cells can express more than one NKG2DL. A two-sided Mann–Whitney U test was used for statistical analysis. k, l, Co-staining of NKG2DLs and LSC markers in CD33+ AML cells (k, n = 9 cases of AML, of which 9 out of 9 cases expressed GPR56 and CD133, and only 3 out of 9 cases expressed CD96) and within CD34+CD38 subpopulations of AML cells (l, n = 5 cases of AML; notably, in the other 7 cases of AML we analysed, all CD34+CD38 cells were found to lack expression of NKG2DLs). A two-sided Student’s t-test was used in k, l. Centre values represent mean, error bars represent s.d. Source Data

Extended Data Fig. 8 PARP1 in human AML: expression, association with clinical outcome and induction of NKG2DLs after PARP1 inhibition.

a, Survival analysis of patients with AML with high (above median, red line) versus low (below median, blue line) expression of PARP1 mRNA (TCGA, n = 179 patients). b, c, Immunoblot analyses of expression of PARP1 protein in NKG2DL compared to NKG2DL+ AML cells (b) and CD34+ compared to CD34 AML cells (c), sorted from the same patient samples. n = 9 for b, n = 3 for c; experiments were repeated twice independently with similar results. GAPDH and actin were used as loading controls. Quantifications are shown in Supplementary Table 6. dh, Treatment with individual (d, n = 3; e, n = 12; f, no. 42) or pooled (g, h, n = 3) PARP1 siRNAs for 24 h inhibits expression of the PARP1 gene (d, g; qRT–PCR, GAPDH used as housekeeping control) and induces surface expression of NKG2DLs on human CD34+ AML cells (e, f, h, no. 38) (control, scrambled non-coding PARP1 siRNAs). Each dot represents a different patient analysed in technical triplicates. i, Analysis of expression of NKG2DLs on engrafted human AML subpopulations (percentage of NKG2DL+ within CD33+, CD33+CD34+ and CD33+CD34 subpopulations derived from mouse bone marrow) after five days of in vivo treatment with AG-14361 or DMSO (n = 10 mice per group, n = 3 cases of AML). j, k, Analysis of surface expression of NKG2DLs after in vitro treatment with AG-14361 (20 μM, 24 h) or DMSO in sorted CD34+ and corresponding CD34 AML cells (j, left, representative results; right, summarized fold changes of NKG2DL+ cells in AG-14361 versus DMSO cultured cells; n = 3 cases of AML) or in bulk AML cells from non-CD34-expressing cases of AML (kn = 10 cases of AML). Summarized fold changes in NKG2DL+ AML cells in PARP inhibition versus corresponding control conditions are shown. l, m, Sorted NKG2DL (top panels) and corresponding NKG2DL+ (bottom panels) AML subpopulations were treated for 24 h with AG-14361 (20 μM) or DMSO (0.2%) and analysed by flow cytometry for MICA, MICB, ULBP1 or ULBP2, ULBP5 or ULBP6 surface expression (l, SFI; no 16, 35 and 151) and using DAPI (m) to determine viability (left) and absolute cell numbers (right) (n = 5 cases of AML). Mean values of technical triplicate analyses are shown. n, Corresponding analyses with healthy CD34+ cells from n = 3 samples of cord blood. o, Leukaemic bone marrow infiltration after in vivo treatment with AG-14361 (days 1 to 5, 10–15 mg kg−1 day−1) or DMSO (days 1 to 5, 20%) in n = 10 mice for each group. Statistical analyses were performed using a log-rank (Mantel–Cox) test (a), a two-sided Mann–Whitney U test (k, o) or a two-sided Student’s t-test (all other plots). Each dot represents the mean of technical triplicates per patient sample. Centre values represent mean, error bars represent s.d. Source Data

Extended Data Fig. 9 Modulation of NKG2DLs.

a, b, Expression of NKG2DLs after treatment of bulk AML cells with retinoic acid (ATRA, 1 μM), valproic acid (VPA, 2 μM), 5-azacytidine (5 μM), AG-14361 (20 μM) or veliparib (10 μM). Quantified summarized fold-changes in CD34+NKG2DL+ and CD34NKG2DL+ populations after 24 h of in vitro treatment (a, n = 3 cases of AML; b, n = 11 cases of AML). All analysed in technical triplicates; DMSO 0.2% or PBS were used as carrier controls. c, Release of soluble NKG2DLs from sorted CD34+ and corresponding CD34 AML subpopulations (‘shedding assays’). n = 8 cases of AML; mean results with s.d. are shown. dg, Baseline mRNA expression of different individual NKG2DLs and their variants. d, Relative expression of single ligands; e, relative summarized ligand expression. n = 10 patients with AML. f, g, Induction of NKG2DL mRNAs after PARP1 inhibition using PARP1 siRNAs (f, 24 h in vitro treatment; control, scrambled non-coding siRNAs) or AG-14361 (g, 20 μM, 24 h in vitro treatment; control, DMSO carrier (0.2%)). Fold changes in relative expression levels of mRNA of individual ligands compared to control treatments in individual patients are shown, as indicated. Note that heterogeneous NKG2DLs are upregulated upon PARP inhibition in different cases of AML. Statistical analyses were performed using a two-sided Mann–Whitney U test (c) or a two-sided Student’s t-test (a, b, dg). Centre values represent mean, error bars represent s.d. Source Data

Extended Data Fig. 10 Treatment with a PARP1 inhibitor suppresses in vivo induction of leukaemia in mice co-transplanted with NK cells, but does not affect expression of NKG2DLs in healthy haematopoietic cells and baseline haematopoiesis.

a, b, Treatment with AG-14361 in vitro (pre-transplantation) or in vivo (post-transplantation) inhibits the capacity for the in vivo initiation of leukaemia of human AML cells in NSG mice co-transplanted with NK cells. a, In vitro pre-treatment: AML cells were cultured in vitro with AG-14361 (20 μM) or DMSO (0.2%) for 24 h and then transplanted via tail vein injection into NSG mice (1.5 × 106 AML cells per mouse), which afterwards were co-transplanted (or not) with pNKCs (1.5 × 107 pNKCs per mouse) (n = 3 mice per condition and patient, n = 5 cases of AML). Mice were analysed for the presence of leukaemic cells in bone marrow, peripheral blood, liver and spleen at 16 h after transplantation. Summarized results of n = 5 independent biological experiments are shown, after normalization to ‘DMSO control without NK cells’ (which was set to 1). Statistical analysis was performed using a two-sided Mann–Whitney U test. b, In vivo treatment: mice transplanted with human AML cells (no. 35, 1.5 × 106 AML cells per mouse, transplanted intrafemorally, n = 6 mice per group) were treated with AG-14361 (10 mg kg-1 intraperitoneally, on days 1 to 5 after transplantation) or DMSO control, and afterwards co-transplanted (or not) with pNKCs (4.5 × 106 pNKCs per mouse administered once intravenously on day 6 after transplantation, pre-treated or not with anti-NKG2D or isotype control, 5 μg ml-1). Mice were analysed at week nine after transplantation for leukaemic engraftment. Note that between day 6 after transplantation and the final analysis time point, no further treatment was applied. See schematic of the experiment and further data with higher (10:1) pNKC:AML cell ratio in Fig. 4j, k. Statistical analyses were performed using a two-sided Student’s t-test. ci, Surface expression of NKG2DLs on healthy human (cf) and mouse (gi) haematopoietic cells at baseline and after PARP1 inhibition. Representative flow cytometry data of the indicated human haematopoietic cells derived from peripheral blood (c) and bone marrow and cord blood (df) of healthy donors, and quantification (f). In g, expression of NKG2DLs is quantified on different subpopulations of healthy mouse haematopoietic bone marrow cells (n = 3 mice; bulk leukaemic cells from Mll-Enl and Mll-ptd/Flt3-ITD mice are shown as positive controls). hj, Treatment of mice with AG-14361 (10 mg kg-1, intraperitoneally) or DMSO vehicle control, and subsequent quantification of expression of NKG2DLs on haematopoietic cells. Schematic of the experiment (h) and quantification of percentages of NKG2DL+ cells among total mouse haematopoietic cells of specific compartments (i) (haematopoietic stem cells (HSCs): KIT+LinSCA1+CD150+CD48; MEP, megakaryocyte–erythroid progenitor; CLP, common lymphoid progenitor; GMP, granulocyte–macrophage progenitor) and absolute numbers of white blood cell counts (j) (with distribution of neutrophils, lymphocytes and monocytes) and red blood cell counts (n = 3 mice per group). Centre values represent mean, error bars represent s.d. Two-sided statistical tests were performed using Mann–Whitney U test (a) or Student’s t-test (b, fj). Centre values represent mean, error bars represent s.d. for all plots. Source Data

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-5.

Reporting Summary

Supplementary Table 1

This file contains patient characteristics.

Supplementary Table 2

This file contains summarized information and engraftment data of NKG2DLneg vs. NKG2DLpos cells transplanted into NSG mice.

Supplementary Table 3

This file contains gene sets enriched in NKG2DLneg compared to NKG2DLpos subpopulations. GSEA was performed using the gene ontology (GO) gene set from the Molecular Signatures Database v4.0 (MSigDB, http://www.broadinstitute.org/gsea/msigdb/collections.jsp#C5).

Supplementary Table 4

This file contains differentially expressed genes obtained from RNAseq-data.

Supplementary Table 5

This file contains log2 fold-changes of overlapping differentially expressed genes per patient from gene expression arrays.

Supplementary Table 6

This file contains quantification of immunoblots.

Supplementary Table 7

In vitro treatment of bulk AML cells with AG-14361 and DMSO control. AML cells were treated for 24h with 20 µM AG-14361 or respectively DMSO control (0.2%) and afterwards stained for NKG2DL, CD33 and CD34 expression. Percentages of %NKG2DLpos cells within each subpopulation are displayed. Mann-Whitney U Test was performed to test for statistical significance.

Supplementary Table 8

This file contains primer sequences.

Source data

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