2012;79:340C350. enhanced stimulation and enrichment efficacy. These EBV-specific epitopes broadening the repertoire of known targets will improve manufacturing of clinically applicable EBV-CTLs and monitoring of EBV-specific T-cell responses in patients. by EBV-infected target cells. To ensure and clinical relevance, EBV-derived peptides were deliberately isolated from EBV-immortalized, HLA-A*03:01-lentivirally transduced B-lymphoblastoid cell lines (B-LCLs), acting as surrogate cells for PTLD . Immunogenicity, cytotoxicity and clinical eligibility of eleven CTL candidate epitopes were evaluated. The newly identified, immunodominant EBV-specific CTL epitopes will improve (1) the accurate monitoring of EBV-specific T-cell immune responses in patients before and after transplantation, (2) the identification of suitable T-cell donors as well as (3) the manufacturing of clinical-grade antiviral T cells in a sufficient cell number for the adoptive transfer to ameliorate the clinical outcome of patients suffering from EBV-related complications. RESULTS Verification of isolated HLA-A*03:01-restricted EBV-derived peptides A combination of different epitope prediction tools was applied to scan the unfiltered sequences of HLA-A*03:01-restricted EBV-derived peptides isolated (Supplementary Figure 1). Among these, only 4.49% of the sequences (= 673) remained after the first sorting exclusively based on the peptide-ion-score. As this particular score is not completely congruous with the quality of the sequence’s MS/MS-spectrum, this relatively low cut-off value was chosen . Resulting from the cut-off value of 15%RANK (NetMHC) 32.4% (= 218) of the 673 ranked sequences remained candidates. Subsequent to the scanning of the candidates by NetMHC, NetCTL and NetMHCstab, the 20 highest scoring sequences of each EBV+B-LCL or those classified as strong [SB] or weak binders [WB] (= 63) were comparatively analyzed by ExPASy-ProtParam-tool and SYFPEITHI. 17.5% of the remaining sequences Tyrphostin AG 183 (= 11) answered the additional criterion of not presenting any homologies to the human genome (Table ?(Table1).1). Most of them derive from proteins associated with either latency and/or reactivation or with potential to promote malignant transformation. In this context A*03_BTRF1FLGK represents the only exception as it derives from EBV protein BTRF1 that has not been characterized yet. Considering the HLA-A*03:01 peptide supermotif with focus on the primary anchor positions P2 and P9 [45, 46], all eleven EBV-peptide sequences carry one of the highly preferred amino acids at P2 (A, I, RAB21 L, T, V, M, S). Eight of them contain the typically preferred residues at P9 (K, R). Taking all the mentioned criteria into account, these eleven EBV-specific peptide-sequences continued to be potentially relevant as novel T-cell epitopes and therefore appropriate for further investigation (Table ?(Table1).1). Four of them were predicted as strong and six of them as weak binders (NetMHC). These predicted binding affinities were confirmed by SYFPEITHI-scores ranging from 20 to 31, except for A*03_BILF2VTLA. Ten EBV-derived sequences were predicted to be potential CTL epitopes by NetCTL with combined scores ranging from 0.748 to 1 1.676. Stability of the pMHC complexes was considered to be either highly or weakly stable (NetMHCstab) in ten of the sequences, confirmed by the instability indices obtained from the ExPASy-ProtParam-tool, classifying all eleven sequences to be stable. In Tyrphostin AG 183 summary, eleven isolated HLA-A*03:01-restricted EBV-derived peptides (Table ?(Table1)1) were found to be potentially relevant according to their respective epitope prediction scores and were therefore further on investigated. Table 1 Tyrphostin AG 183 isolated, highly scored EBV-specific candidate-epitopesCpredicted results and IFN- EliSpot-based screening for immunogenicity A*03_BPLF1KLLRLarge tegument protein deneddylaseCBPLF113.570.01SB1.6755E0.785SB HS38.79stable355/14TVARHLLGAKA*03_BALF5TVARDNA polymerase catalytic protein – BALF513.300.15SB0.7951E0.586SB WS19.77stable267/14ATGMVPAVKKA*03_BBRF1ATGMPortal protein UL6 homologCBBRF128.730.20SB0.9726E0.431WB36.15stable202/10KLVCSEPLVK[024, 623]A*03_BcRF1KLVCTBP-like protein – BcRF130.290.40SB0.9152E0.597WB WS36.15stable315/14VTLAHAGYYA*03_BILF2VTLA (1),(2)GlycoproteinCBILF249.380.70WB1.2361E0.419WBC5.70stable1413/21FLLAMTSLRA*03_BcRF1FLLA (1),(2)TBP-like proteinCBcRF112.900.70WB1.4480E0.347WB27.09stable2113/19FLGKYIKVKKA*03_BTRF1FLGKA*03_BALF3QVAT (1),(2)Tripartite terminase subunit UL28 homologCBALF318.171.20WB0.9267E0.414WB WS21.91stable3012/19TLVDVRAIKA*03_BaRF1TLVDRibonucleoside-diphosphate reductase small chainCBaRF116.601.20WB1.0387E0.415WBC17.24stable265/14KIVTNILIYA*03_gBKIVTenvelope glycoprotein BCgB10.091.30WB1.2615E0.346WB34.11stable202/10LIIPNVTLAHA*03_BILF2LIIP(2)GlycoproteinCBILF249.384.000.74760.239C10.86stable2211/20 Open in a separate window [aa] = amino acid, [B-LCL] = B-lymphoblastoid cell line, (1) = component of EBV_Consensus+3PMIX, (2) = component of EBV_Consensus+4PMIX, [Ref.] = References, [pep_score] = peptide score (sequences probability of an existent match to a database entry), [BL] = Binding Level, [SB] = strong binder, [WB] = weak binder, [HS] = highly stable binder, [WS] = weakly stable binder, [score] = combined prediction score, [E] = identified as potential CTL epitope, [Instab.-Index] = Instability Index, [class.] = classification. Overview of the eleven investigated HLA-A*03:01-restricted candidate-epitopes and.