| Literature DB >> 25992555 |
Kateřina Kuželová1, Barbora Brodská1, Ota Fuchs2, Marie Dobrovolná3, Petr Soukup4, Petr Cetkovský4.
Abstract
Nucleophosmin 1 (NPM1) mutations are frequently found in patients with acute myeloid leukemia (AML) and the newly generated sequences were suggested to induce immune response contributing to the relatively favorable outcome of patients in this AML subset. We hypothesized that if an efficient immune response against mutated nucleophosmin can be induced in vivo, the individuals expressing HLA alleles suitable for presenting NPM-derived peptides should be less prone to developing AML associated with NPM1 mutation. We thus compared HLA class I frequencies in a cohort of patients with mutated NPM1 (63 patients, NPMc+), a cohort of patients with wild-type NPM1 (94 patients, NPMwt) and in normal individuals (large datasets available from Allele Frequency Net Database). Several HLA allelic groups were found to be depleted in NPMc+ patients, but not in NPMwt compared to the normal distribution. The decrease was statistically significant for HLA B(*)07, B(*)18, and B(*)40. Furthermore, statistically significant advantage in the overall survival was found for patients with mutated NPM1 expressing at least one of the depleted allelic groups. The majority of the depleted alleles were predicted to bind potent NPM-derived immunopeptides and, importantly, these peptides were often located in the unmutated part of the protein. Our analysis suggests that individuals expressing specific HLA allelic groups are disposed to develop an efficient anti-AML immune response thanks to aberrant cytoplasmic localization of the mutated NPM protein.Entities:
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Year: 2015 PMID: 25992555 PMCID: PMC4439052 DOI: 10.1371/journal.pone.0127637
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Fig 1Comparison of HLA class I profiles in AML patients and in normal individuals.
HLA class I profiles in normal European population (clear bars), in AML patients with C-terminal NPM1 mutations (black bars) and in AML patients with wild-type NPM1 (cross-hatched bars). The normal allele distribution is represented by the means from two large datasets obtained from neighbouring white populations. Differences in allele frequencies between groups were statistically evaluated using contingency tables. Statistically significant differences (p < 0.05) are marked with asterisks.
Characteristics of NPMc+ AML patient groups.
| group 1 | group 2 | |
|---|---|---|
| Patient number | N = 41 | N = 19 |
| Age at diagnosis: mean | 50.6 | 49.2 |
| Age at diagnosis: range | 24 to 64 | 24 to 65 |
| % of Flt3-ITD positive cases | 51% (20/39, 2 not tested) | 44% (7/16, 3 not tested) |
| % of DNMT3 mutated cases | 71% (25/35, 6 not tested) | 75% (12/16, 3 not tested) |
| % of transplanted | 59% (24/41) | 26% (5/19) |
| % of relapsed | 44% (18/41) | 63% (12/19) |
NPMc+ AML patients were divided into two groups on the basis of HLA typing. Group 1 includes patients bearing at least one of the following allelic groups: A*03, A*11, B*07, B*18, B*39, B*40, C*03, C*07. Group 2 includes patients not having any of these alleles. All patients were treated using the same standard protocols.
Fig 2Overall survival of AML patients with different HLA types.
Group 1 (red) includes patients bearing at least one of the following allelic groups: HLA-A*03, A*11, B*07, B*18, B*39, B*40, C*03 or C*07. Patients in the group 2 (black) express none of these HLA alleles. The survival time from the day of diagnosis was evaluated. All patients were treated using the same standard protocol. Panel A: Patients with mutated NPM1 (NPMc+). The basic characteristics of the NPMc+ patient groups are given in Table 1. Panel B: Patients with wild-type NPM1.
Immunopeptides (8-11AA) derived from the mutated C-terminus of NPM.
| allele | peptide length | start | end | sequence | perc. rank | IC50 (nM) | SYFPEITHI score |
|---|---|---|---|---|---|---|---|
| C*03:03 | 8 | 289 | 296 | LAVEEVSL | 0.3 | 3 | - |
| C*03:04 | 8 | 289 | 296 | LAVEEVSL | 0.4 | - | - |
| B*35:03 | 8 | 289 | 296 | LAVEEVSL | 0.5 | 2264 | - |
| B*37:01 | 11 | 281 | 291 | QEAIQDLCLAV | 0.7 | - | - |
| A*11:01 | 9 | 290 | 298 | AVEEVSLRK | 0.75 | 35 | 27 |
| A*68:01 | 9 | 289 | 297 | LAVEEVSLR | 0.8 | 30 | 20 |
| B*40:01 | 9 | 281 | 289 | QEAIQDLCL | 0.9 | 313 | 24 |
| B*49:01 | 11 | 281 | 291 | QEAIQDLCLAV | 0.9 | - | - |
| B*40:02 | 11 | 281 | 291 | QEAIQDLCLAV | 0.9 | 360 | - |
Immune Epitope Database (IEDB) was used to predict immunopeptides derived from the mutated sequence of type A mutated NPM. The cutoff value of percentile rank was set to 1%. IC50 values were calculated using ANN tool embedded in IEDB. When available, scores according to SYFPEITHI database are also given for the predicted peptides.
Predicted immunopeptides (8–11 AA) derived from the unmutated NPM sequence.
| allele | peptide length | start | end | sequence | perc. rank | IC50 (nM) | SYFPEITHI score |
|---|---|---|---|---|---|---|---|
|
| |||||||
| A*68:01 | 9 | 265 | 273 | EAKFINYVK | 0.2 | 8 | 19 |
| A*30:01 | 9 | 221 | 229 | RSKGQESFK | 0.2 | 4 | - |
| A*68:01 | 10 | 268 | 277 | FINYVKNCFR | 0.3 | 8 | 15 |
| A*30:01 | 8 | 195 | 202 | SIRDTPAK | 0.3 | 7 | - |
| A*68:01 | 11 | 3 | 13 | DSMDMDMSPLR | 0.3 | 10 | 19 |
| A*68:01 | 9 | 93 | 101 | EITPPVVLR | 0.35 | 12 | 28 |
| A*30:01 | 9 | 194 | 202 | KSIRDTPAK | 0.4 | 8 | - |
| A*31:01 | 10 | 268 | 277 | FINYVKNCFR | 0.4 | 18 | - |
| A*31:01 | 9 | 269 | 277 | INYVKNCFR | 0.5 | 12 | - |
| A*02:01 | 9 | 17 | 25 | YLFGCELKA | 0.6 | 12 | 22 |
| A*11:01 | 9 | 194 | 202 | KSIRDTPAK | 0.65 | 27 | 21 |
| A*30:01 | 8 | 248 | 255 | KAKMQASI | 0.7 | 23 | - |
| A*68:01 | 11 | 63 | 73 | EAMNYEGSPIK | 0.7 | 26 | 18 |
| A*68:01 | 9 | 81 | 89 | MSVQPTVSL | 0.8 | 15 | 8 |
| A*68:01 | 8 | 17 | 24 | YLFGCELK | 0.8 | 31 | - |
| A*30:01 | 11 | 101 | 111 | RLKCGSGPVHI | 0.8 | 35 | - |
| A*11:01 | 10 | 64 | 73 | AMNYEGSPIK | 0.85 | 48 | 19 |
| A*30:01 | 8 | 73 | 80 | KVTLATLK | 0.9 | 35 | - |
| A*30:01 | 8 | 148 | 155 | GSKVPQKK | 0.9 | 34 | - |
|
| |||||||
| B*39:01 | 10 | 40 | 49 | HQLSLRTVSL | 0.1 | 8 | 17 |
| B*40:01 | 9 | 92 | 100 | FEITPPVVL | 0.2 | 8 | 30 |
| B*07:02 | 10 | 70 | 79 | SPIKVTLATL | 0.2 | 14 | 22 |
| B*18:01 | 9 | 36 | 44 | DENEHQLSL | 0.25 | 13 | 25 |
| B*07:02 | 10 | 219 | 228 | TPRSKGQESF | 0.25 | 29 | 18 |
| B*39:01 | 9 | 92 | 100 | FEITPPVVL | 0.3 | 18 | 16 |
| B*08:01 | 9 | 41 | 49 | QLSLRTVSL | 0.3 | 40 | 26 |
| B*40:01 | 11 | 62 | 72 | AEAMNYEGSPI | 0.3 | 16 | - |
| B*40:01 | 11 | 92 | 102 | FEITPPVVLRL | 0.3 | 16 | - |
| B*39:01 | 11 | 79 | 89 | LKMSVQPTVSL | 0.4 | 28 | - |
| B*39:01 | 9 | 276 | 284 | FRMTDQEAI | 0.45 | 19 | 16 |
| B*07:02 | 9 | 10 | 18 | SPLRPQNYL | 0.5 | 31 | 23 |
| B*07:02 | 9 | 70 | 78 | SPIKVTLAT | 0.5 | 19 | 21 |
| B*39:01 | 10 | 70 | 79 | SPIKVTLATL | 0.5 | 39 | 13 |
| B*39:01 | 11 | 39 | 49 | EHQLSLRTVSL | 0.5 | 46 | - |
| B*07:02 | 11 | 13 | 23 | RPQNYLFGCEL | 0.55 | 16 | - |
| B*15:01 | 8 | 221 | 228 | RSKGQESF | 0.6 | 47 | - |
| B*58:01 | 8 | 24 | 31 | KADKDYHF | 0.6 | 38 | - |
|
| |||||||
| C*05:01 | 8 | 24 | 31 | KADKDYHF | 0.2 | 3 | - |
| C*15:02 | 10 | 142 | 151 | RSAPGGGSKV | 0.3 | 42 | - |
| C*05:01 | 10 | 278 | 287 | MTDQEAIQDL | 0.3 | 11 | - |
| C*07:01 | 8 | 109 | 116 | VHISGQHL | 0.3 | 27 | - |
| C*06:02 | 9 | 276 | 284 | FRMTDQEAI | 0.35 | 35 | - |
| C*05:01 | 11 | 32 | 42 | KVDNDENEHQL | 0.5 | 45 | - |
| C*07:01 | 9 | 276 | 284 | FRMTDQEAI | 0.55 | 32 | - |
| C*12:03 | 8 | 65 | 72 | MNYEGSPI | 0.6 | 23 | - |
| C*12:03 | 10 | 63 | 72 | EAMNYEGSPI | 0.8 | 29 | - |
| C*15:02 | 10 | 74 | 83 | VTLATLKMSV | 0.8 | 93 | - |
| C*14:02 | 11 | 66 | 76 | NYEGSPIKVTL | 0.8 | 26 | - |
| C*03:03 | 11 | 47 | 57 | VSLGAGAKDEL | 0.8 | 11 | - |
| C*03:03 | 9 | 92 | 100 | FEITPPVVL | 0.9 | 8 | - |
| C*03:03 | 11 | 92 | 102 | FEITPPVVLRL | 0.9 | 13 | - |
Immune Epitope Database (IEDB) was used to predict immunopeptides derived from the whole sequence of type A mutated NPM. The cutoff value of percentile rank was set to 1% and the resulting peptide sets were restricted to high-affinity peptides (IC50 less than 50 nM). When available, scores according to SYFPEITHI database are also given for the predicted peptides.