TARP is an immunotherapeutic target in acute myeloid leukemia expressed in the leukemic stem cell compartment

Abstract

Immunotherapeutic strategies targeting the rare leukemic stem cell compartment might provide salvage to the high relapse rates currently observed in acute myeloid leukemia (AML). We applied gene expression profiling for comparison of leukemic blasts and leukemic stem cells with their normal counterparts. Here, we show that the T-cell receptor γ chain alternate reading frame protein (TARP) is over-expressed in de novo pediatric (n=13) and adult (n=17) AML sorted leukemic stem cells and blasts compared to hematopoietic stem cells and normal myeloblasts (15 healthy controls). Moreover, TARP expression was significantly associated with a fms-like tyrosine kinase receptor-3 internal tandem duplication in pediatric AML. TARP overexpression was confirmed in AML cell lines (n=9), and was found to be absent in B-cell acute lymphocytic leukemia (n=5) and chronic myeloid leukemia (n=1). Sequencing revealed that both a classical TARP transcript, as described in breast and prostate adenocarcinoma, and an AML-specific alternative TARP transcript, were present. Protein expression levels mostly matched transcript levels. TARP was shown to reside in the cytoplasmic compartment and showed sporadic endoplasmic reticulum co-localization. TARP-T-cell receptor engineered cytotoxic T-cells in vitro killed AML cell lines and patient leukemic cells co-expressing TARP and HLA-A*0201. In conclusion, TARP qualifies as a relevant target for immunotherapeutic T-cell therapy in AML.

Figure 1

T-cell receptor γ chain alternate reading frame protein (TARP) transcript expression in pediatric acute myeloid leukemia (pedAML) and adult AML leukemic cells and cell lines. For TARP qualitative polymerase chain reaction (qPCR), (CNRQ) values were calculated using LNCaP (prostate adenocarcinoma cell line) as interrun calibrator. Biological replicates, e.g. cells sorted from the same patient in different runs and independent cDNA syntheses, were depicted as independent data points. Horizontal bars indicate means and error bars indicate mean±standard error or mean (SEM). Horizontal square brackets represent statistical comparisons; *P<0.05; **P<0.01; ***P<0.001; ****P<0.0001. (A) TARP expression was determined in CD34⁺CD38⁺ (n=4) and CD34⁺CD38⁻ (n=3) cell fractions from four pedAML patients (2 FLT3-ITD, 2 FLT3 WT) (Online Supplementary Table S1) by micro-array profiling. Sorted CD34⁺CD38⁺ (n=3) and CD34⁺CD38- (n=2) cord blood (CB) cells were used as control populations. Mean log2-FC values (y-axis) were calculated based on both TARP probes included in the array, the x-axis represents the different sample groups. (B) TARP expression was significantly higher in CD34⁺CD38⁻ and CD34⁺CD38⁺ cell fractions from AML patients (13 pedAML and 17 adult AML) compared to healthy controls (7 CB, 6 NBM and 2 mPBSC) (P<0.01, Mann Whitney U test). Blasts from NBM showed a marginally higher expression compared to CB (P=0.049). (C) Comparison of TARP expression between leukemic stem cells (LSC) and blasts within pedAML (circles, n=10) and adult AML (squares, n=12) on a per patient basis showed no significant differences (P>0.05, paired sample t-test). (D) Bars display the percentage of patients (%), harboring the characteristic shown in the x-axis (dichotomous variables, for details see Table 1), for TARP-high (black, n=8) and TARP-low (white, n=5) pedAML patients. The total number of patients positive for each characteristic is shown between parentheses. Patients without central nervous system (CNS) involvement all showed negative lumbar punctures. Data on CNS involvement and risk profile is lacking for one patient. The number of patients harboring FLT3-ITD (P<0.001) and HR profiles (P<0.05) were significantly higher in the TARP-high group, whereas TARP-low pedAML patients included significantly more CBF-leukemia (P<0.01) and SR profiles (P<0.05) (χ² test). (E) Differential TARP expression between LSC and blasts sorted from pediatric and adult AML patients with FLT3-ITD versus FLT3 WT. A significant higher TARP expression in LSC (P<0.01) and blasts (P<0.0001) was only detected for FLT3-ITD positive pedAML patients (Mann Whitney U test). (F) TARP expression in nine AML cell lines, five B-ALL cell lines, the CML cell line K562, the Epstein-Barr virus (EBV)-immortalized B-cell line JY and T2 cell line, next to two breast (BT-474, MCF-7) and two prostate (LNCaP, PC3) adenocarcinoma cell lines. Dashed lines indicate the expression observed in PC3 and LNCaP, serving as low and high reference, respectively, in agreement with previous literature. (G) Delta (d) Ct values were calculated for TARP, MALAT1 and TBP between cytoplasmic and nuclear compartments of THP-1 and LNCaP, in order to examine the subcellular location of TARP. THP-1 showed a cytoplasmic residence for TARP, in agreement with LNCaP. FC: fold change; FT: fusion transcript; Kas-1: Kasumi-1; MM-6: MONO-MAC6; mPBSC: mobilized peripheral blood stem cells; NBM: normal bone marrow.

Figure 2

T-cell receptor γ chain alternate reading frame protein (TARP) expression in cell lines evaluated by western blotting. Whole-blot images with ladders used for size estimation are shown in Online Supplementary Figure S7. (A) TARP transgenic (OE) cell lines generated for OCI-AML3 and THP-1 showed a 27 kDa protein for GFP and a 15-25 kDa protein for TARP. In agreement with low TARP transcript levels, the OCI-AML3 mock cell line only showed a 27 kDa GFP protein. TARP expression in THP-1 OE was higher than OCI-AML3 OE, most likely resulting from both transgenic and cognate TARP protein expression, since THP-1 was categorized by qualitative polymerase chain reaction (qPCR) as a TARP-high acute myeloid leukemia (AML) cell line. (B) Immunoblotting of TARP and β-actin in AML cell lines (HL-60, Kg-1a, MOLM-13, OCI-AML3, MV4;11 and THP-1) next to LNCaP. Protein expression mostly matched transcript levels, except for Kg-1a, although confocal microscopy did allow TARP protein staining in Kg-1a. β-actin expression appeared to be lower for LNCaP and MOLM-13, although equal amounts of protein were loaded. (C) Immunoblotting of TARP and β-actin in selected shRNA-mediated knockdown (KD) AML cell lines for MV4;11, HL-60 and THP-1, next to their respective mock and wild-type (WT) cell line. For HL-60, a stable knockdown was introduced by shRNA 3 (19.4% compared to mock). KD: knockdown; OE: overexpression.

Figure 3

T-cell receptor γ chain alternate reading frame protein (TARP) protein detection in Kg-1a and patient leukemic cells by confocal microscopy. Merged patterns visualize TARP (red) and HSP-60 (top lane) or calnexin (bottom lane) (both in green) co-localization (yellow fusion signals) together with DAPI nuclear counter-staining (blue). Leukemic cells were sorted from two pediatric acute myeloid leukemia (pedAML) patients, classified as TARP-high and TARP-low by qualitative polymerase chain reaction. Calnexin staining was not performed on primary cells due to lack of material. Within Kg-1a and the sorted TARP-high leukemic cells, TARP expression was enriched at the cells’ protrusions, indicated by arrows.

Figure 4

Functional evaluation of T-cell receptor (TCR)-transgenic cytotoxic T cells (CTL) towards cognate and modified cell lines and patient leukemic cells. (A) Cytokine response (IFN-γ/IL-2 expression within the CD3⁺/CD8⁺ compartment) by co-incubation (1 hour, h) with OCI-AML3 and THP-1 was evaluated by both lentiviral (LV) and retroviral (RV) TCR-T-cell receptor γ chain alternate reading frame protein (TARP) CTL. LNCaP and patient leukemic cells (single experiment) were only evaluated by LV transduced TARP-TCR CTL. For each target, positive (+) or negative (−) HLA-A*0201 and TARP expression, in this respective order, is indicated between brackets. HLA-A*0201 and TARP co-expressing cell lines (LNCaP and THP-1) were unable to trigger higher cytokine release than OCI-AML3 with low TARP expression. Leukemic cells from a TARP-high pediatric acute myeloid leukemia (pedAML) patient triggered a 2-fold higher cytokine release compared to a TARP-low pedAML patient. (B) Lytic response of LV and RV TARP-TCR CTL versus HLA-A*0201-positive TARP-high (black symbols) and TARP-low (white symbols) targets, measured by a chromium release assay after 4 h. Highest lysis of TARP-high cell lines was observed at E/T ratio 50/1 for LV and 10/1 for RV TARP-TCR CTL (percentages indicated between brackets), whereas OCI-AML3 (HLA-A*0201⁺, TARP⁻) remained unaffected. (C) Lytic response of LV and RV TARP-TCR CTL versus towards wild-type (WT), transgenic and pulsed AML cell lines, measured by a 48-h FCM-based cytotoxicity assay. The dashed line indicates the highest level of non-TARP mediated background killing observed for LV TARP-TCR CTL, as no mock CTL could be constructed. Positive (+) or negative (⁻) expression for HLA-A*0201 and TARP is shown, in this respective order, between brackets. Bold symbols indicate the expression differing from wild-type, either by retroviral transduction or pulsing. HLA-A*0201 transgenic AML cell lines were more efficiently lysed compared to their HLA-A*0201-negative counterparts (Kg-1a, MOLM-13, HL-60). Higher lysis was observed for transgenic TARP OE or peptide-pulsed cell lines compared to the WT cell line (OCI-AML3, THP-1), except for killing of TARP OE OCI-AML3 cell line by RV TARP-TCR CTL. (D) Lysis by LV TARP-TCR CTL, measured at different time points (8h, 24h, 48h and 56h, as indicated on x-axis), based on the luminescence release by transgenic HLA-A*0201-expressing TARP-high AML cell lines with respect to the HLA-A*0201 WT cell line (HL-60-Luc, MOLM-13-Luc and MV4;11-Luc: black symbols). In addition, lysis of the TARP-low, cognate HLA-A*0201-positive OCI-AML3 cell line was evaluated (white symbols). Mean lysis (%) observed after 48 h is indicated next to whiskers, representing the mean±standard error of mean. (E) 48-h FCM-based cytotoxicity assay evaluating lysis of primary leukemic cells (adult AML=5, all FLT3-ITD mutated) by LV TARP-TCR transduced CTL (biological duplicates). TARP transcript expression (CNRQ) is shown in the x-axis for each target. IFN-γ: interferon gamma; IL-2: interleukin-2; INF: influenza.