Background
Materials and methods
Cell culture
Sample information | Cell populations in non-treated sample (% of total) | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID | Group | Karyotype | FLT3 | NPM1 | Blasts | B cells | Mono-cytes | pDCs | NK cells | NKT cells | DNT cells MC15 | DNT cells MC3 | CD4+CD7− T cells | CD4+ T cells | CD8+ T cells |
P1 | AML patient | Complexa | Wt | Wt | 6.25 | 1.45 | 52.61 | 0 | 7.98 | 10.38 | 0 | 0 | 4.34 | 16.98 | 0 |
P2 | AML patient | Complex | ITD | Ins | 52.42 | 0.43 | 8.56 | 0.21 | 3.01 | 16.87 | 0 | 0 | 2.21 | 10.52 | 0 |
P3 | AML patient | Complex | Wt | Wt | 34.22 | 0.62 | 4.70 | 0 | 0 | 6.28 | 0 | 22.19 | 18.64 | 0 | 13.35 |
P4 | AML patient | Complex | Wt | Wt | 96.89 | 0 | 0 | 0.65 | 0 | 0 | 0 | 0 | 0 | 0 | 2.45 |
P5 | AML patient | Complex | Wt | Ins | 82.10 | 4.99 | 0 | 0.22 | 0 | 0 | 0 | 9.19 | 0.08 | 2.05 | 1.37 |
P6 | AML patient | Complex | Wt | Wt | 90.85 | 0.70 | 0 | 0.37 | 0 | 0 | 0 | 5.69 | 0 | 0 | 2.39 |
P7 | AML patient | Normal | Wt | Wt | 82.22 | 0 | 0 | 0 | 0 | 0 | 0 | 14.84 | 0 | 0 | 2.94 |
P8 | AML patient | Normal | ITD | Ins | 90.36 | 0 | 0 | 0.50 | 0 | 0 | 0 | 6.59 | 0 | 0 | 2.55 |
P9 | AML patient | Normal | ITD | Ins | 86.33 | 2.80 | 0 | 0.25 | 0 | 0 | 0 | 7.18 | 0.20 | 0 | 3.24 |
P10 | AML patient | Normal | ITD | Ins | 95.46 | 0 | 0 | 0 | 0 | 0 | 0 | 4.54 | 0 | 0 | 0 |
P11 | AML patient | Normal | ITD | Wt | 95.64 | 0 | 1.09 | 0 | 0 | 0 | 0 | 3.27 | 0 | 0 | 0 |
P12 | AML patient | Normal | ITD | Ins | 97.11 | 0.59 | 0 | 0.24 | 0 | 0 | 0 | 1.32 | 0 | 0 | 0.74 |
D1 | Healthy donor | Normal | Wt | Wt | – | 6.27 | 5.18 | 0.08 | 22.2 | 16.24 | 2.5 | 12.77 | 3.42 | 24.42 | 6.43 |
D2 | Healthy donor | Normal | Wt | Wt | – | 7.64 | 3.49 | 0.31 | 19.27 | 13.05 | 8.16 | 6.74 | 5.50 | 16.40 | 18.23 |
D3 | Healthy donor | Normal | Wt | Wt | – | 9 | 1.64 | 0.23 | 9.69 | 15.40 | 3.47 | 22.25 | 3.47 | 29.50 | 5.18 |
D4 | Healthy donor | Normal | Wt | Wt | – | 9.07 | 0.63 | 0 | 24 | 19.04 | 0.42 | 3.91 | 4.46 | 38.46 | 0 |
D5 | Healthy donor | Normal | Wt | Wt | – | 7.27 | 2.30 | 0.24 | 8.62 | 15.35 | 6.65 | 1.34 | 4.55 | 52.36 | 0 |
Staining of primary cells for mass cytometry (CyTOF)
Phospho-flow cytometry staining and analysis
Viability and cell death assays
IMAC phosphoprotein purification, two-dimensional differential gel electrophoresis, gel analysis and protein identification by mass spectrometry (IMAC/2D DIGE/MS)
Animals
Results
Phosphoproteome analysis of IFNα-Le and IFNα-2b
No. | Protein | UniProtKB ID | DeCyder number | p value | Fold change | Biological process |
---|---|---|---|---|---|---|
250 IU/mL IFNα-2b | ||||||
1 | 14-3-3 protein epsilon (YWHAE) | P62258 | 2864 | 0.016 | 1.45 | Cell cycle transition, apoptosis, membrane organization |
2 | Armadillo repeat-containing protein 6 (ARMC6) | Q6NXE6 | 1602 | 0.017 | − 1.32 | Unknown |
3 | Nascent polypeptide-associated complex subunit alpha (NACA) | Q13765 | 2377 | 0.02 | − 1.44 | DNA dependent transcription, translation |
4 | Vacuolar protein sorting-associated protein 4B (VPS4B) | O75351 | 1659 | 0.023 | − 1.30 | Cell cycle, ATP catabolic process |
5 | 40S ribosomal protein S4, X isoform (RPS4X) | P62701 | 2772 | 0.025 | 1.44 | Translation, positive regulation of proliferation |
6 | UBX domain-containing protein 1 (UBXN1) | Q04323 | 2165 | 0.026 | 1.60 | Negative regulation of protein ubiquitination |
7 | Triosephosphate isomerase (TPI1) | P60174 | 2942 | 0.029 | 1.40 | Glycolysis, metabolic process |
8 | Ras-related protein Rab-11B (RAB11B) | Q15907 | 3213 | 0.032 | − 1.58 | GTPase mediated signal transduction, cell cycle |
9 | 26S protease regulatory subunit 7 (PSMC2) | P35998 | 1805 | 0.039 | − 1.84 | DNA damage response, negative regulation of apoptosis, cell cycle transition |
10 | F-actin-capping protein subunit alpha-1 (CAPZA1) | P52907 | 2493 | 0.047 | − 1.42 | Actin cytoskeleton organization, blood coagulation, immune response |
11 | 40S ribosomal protein SA (RPSA) | P08865 | 2087 | 0.047 | − 1.30 | Translation, RNA metabolic process |
2000 IU/mL IFNα-2b | ||||||
1 | Nascent polypeptide-associated complex subunit alpha (NACA) | Q13765 | 2377 | 0.011 | − 1.31 | DNA dependent transcription, translation |
2 | Alpha-enolase (ENO1) | P06733 | 1789 | 0.017 | − 1.31 | Glycolysis, negative regulation of cell growth |
3 | T-complex protein 1 subunit alpha (TCP1) | P17987 | 1355 | 0.021 | − 1.35 | Protein folding, tubulin complex assembly, cellular protein metabolic process |
4 | Peroxiredoxin-2 (PRDX2) | P32119 | 3214 | 0.023 | − 1.30 | Response to oxidative stress, negative regulation of apoptosis |
5 | Adenylate kinase 2 (AK2) | P54819 | 2753 | 0.047 | 1.37 | ATP metabolic process, oxidative phosphorylation |
6 | 40S ribosomal protein SA (RPSA) | P08865 | 2087 | 0.05 | − 1.55 | Translation, RNA metabolic process |
250 IU/mL IFNα-Le | ||||||
1 | Protein disulfide-isomerase (P4HB) | P07237 | 1663 | 0.00028 | 1.46 | Protein folding, lipoprotein metabolic process, cell redox homeostasis |
2 | T-complex protein subunit zeta (CCT6A) | P40227 | 1137 | 0.003 | − 1.52 | Protein folding, protein transport |
3 | F-actin-capping protein subunit beta (CAPZB) | P47756 | 2679 | 0.0063 | 1.43 | Actin cytoskeleton organization, blood coagulation |
4 | L-lactate dehydrogenase B chain (LDHB) | P07195 | 2474 | 0.0067 | − 1.34 | Glycolysis, oxidation–reduction process |
5 | F-actin-capping protein subunit beta (CAPZB) | P47756 | 2719 | 0.009 | 1.41 | Actin cytoskeleton organization, blood coagulation |
6 | U1 small nuclear ribonucleoprotein A (SNRPA) | P09012 | 2589 | 0.0099 | 1.30 | Gene expression, nuclear mRNA splicing |
7 | Aldose reductase (AKR1B1) | P15121 | 2292 | 0.011 | − 1.31 | Response to stress, carbohydrate metabolic process, daunorubicin and doxorubicin metabolic process |
8 | UBX domain-containing protein 1 (UBXN1) | Q04323 | 2165 | 0.015 | 1.89 | Negative regulation of protein ubiquitination |
9 | F-actin-capping protein subunit alpha-1 (CAPZA1) | P52907 | 2493 | 0.016 | − 1.56 | Glycolysis, oxidation–reduction process |
10 | Triosephosphate isomerase (TPI1) | P60174 | 2942 | 0.016 | 1.56 | Glycolysis, metabolic process |
11 | Isocitrate dehydrogenase (NAD) subunit alpha (IDH3A) | P50213 | 2367 | 0.021 | − 1.46 | Carbohydrate metabolic process, oxidation–reduction process |
12 | Actin, cytoplasmic 2 (ACTG1) | P63261 | 2075 | 0.022 | − 1.60 | Immune response, cellular membrane organization |
13 | L-lactate dehydrogenase B chain (LDHB) | P07195 | 2331 | 0.022 | − 1.31 | Glycolysis, oxidation–reduction process |
14 | Pyruvate kinase isozymes M1/M2 (PKM2) | P14618 | 1380 | 0.026 | − 1.41 | Response to hypoxia, programmed cell death, ATP biosynthetic process |
15 | Pyruvate kinase isozymes M1/M2 (PKM2) | P14618 | 1381 | 0.028 | − 1.43 | Response to hypoxia, programmed cell death, ATP biosynthetic process |
16 | N-alpha-acetyltransferase 10 (NAA10) | P41227 | 2695 | 0.028 | − 1.46 | Protein amino acid acetylation |
17 | Annexin A2 (ANXA2) | P07355 | 2977 | 0.036 | − 1.36 | Angiogenesis, collagen fibril organization |
2000 IU/mL IFNα-Le | ||||||
1 | 14-3-3 protein epsilon (YWHAE) | P62258 | 2864 | 0.00047 | 1.53 | Cell cycle transition, apoptosis, membrane organization |
2 | F-actin-capping protein subunit beta (CAPZB) | P47756 | 2679 | 0.0012 | 1.60 | Actin cytoskeleton organization, blood coagulation |
3 | Heat shock protein 105 kDa (HSPH1) | Q92598 | 436 | 0.016 | 1.34 | Unfolded protein response, positive regulation of NK cell activation |
4 | Acidic leucine-rich nuclear phosphoprotein 32 family member A (ANP32A) | P39687 | 2739 | 0.018 | 1.36 | Regulation of DNA dependent gene expression, RNA metabolic process |
5 | Actin, cytoplasmic 2 (ACTG1) | P63261 | 2075 | 0.029 | − 1.36 | Immune response, cellular membrane organization |
No. | Protein | UniProtKB ID | DeCyder number | p value | Fold change | Biological process |
---|---|---|---|---|---|---|
250 IU/mL IFNα-Le versus IFNα-2b | ||||||
1 | L-lactate dehydrogenase B chain (LDHB) | P07195 | 2331 | 0.00019 | 1.41 | Glycolysis, oxidation–reduction process |
2 | Aldose reductase (AKR1B1) | P15121 | 2292 | 0.00079 | 1.31 | Response to stress, carbohydrate metabolic process |
3 | N-alpha-acetyltransferase 10 (NAA10) | P41227 | 2695 | 0.0039 | 1.32 | Protein amino acid acetylation |
4 | Pyruvate kinase isozymes M1/M2 (PKM2) | P14618 | 1376 | 0.03 | 1.40 | Response to hypoxia, programmed cell death, ATP biosynthetic process |
5 | Catalase (CAT) | P04040 | 646 | 0.038 | 1.30 | Hydrogen peroxide catabolic process, negative regulation of apoptosis, cell division |
6 | Pyruvate kinase isozymes M1/M2 (PKM2) | P14618 | 1381 | 0.04 | 1.39 | Response to hypoxia, programmed cell death, ATP biosynthetic process |
7 | 26S protease regulatory subunit 7 (PSMC2) | P35998 | 1805 | 0.05 | − 1.76 | DNA damage response, negative regulation of apoptosis, cell cycle transition |
2000 IU/mL IFNα-Le versus IFNα-2b | ||||||
1 | 14-3-3 protein epsilon (YWHAE) | P62258 | 2864 | 0.00014 | − 1.47 | Cell cycle transition, apoptosis, membrane organization |
2 | 28S ribosomal protein 23 (MRPS23) | Q9Y3D9 | 3180 | 0.00032 | − 1.30 | Translation |
3 | 40S ribosomal protein S4, X isoform (RPS4X) | P62701 | 2797 | 0.00093 | 1.36 | Translation, positive regulation of proliferation |
4 | Plastin-2 (LCP1) | P13796 | 1244 | 0.0015 | − 1.48 | Protein folding, response to stress, cell cycle, ATP catabolic process |
5 | Sorting nexin-5 (SNX5) | Q9Y5X3 | 1628 | 0.0057 | − 1.43 | Protein transport, cell communication |
6 | Acidic leucine-rich nuclear phosphoprotein 32 family member A (ANP32A) | P39687 | 2739 | 0.0076 | − 1.56 | Regulation of DNA dependent gene expression, RNA metabolic process |
7 | Transgelin-2 (TAGLN2) | P37802 | 3189 | 0.0077 | − 1.43 | Actin organization, muscle organ development |
8 | Heat shock protein HSP 90-beta (HSP90AB1) | P08238 | 829 | 0.0097 | − 1.51 | Protein folding, response to stress, activation of innate immune response, regulation of type I IFN mediated signaling pathway |
9 | Alpha-enolase (ENO1) | P06733 | 1789 | 0.013 | − 1.50 | Glycolysis, negative regulation of cell growth |
10 | Protein deglycase DJ-1 (PARK7) | Q99497 | 3207 | 0.015 | − 1.39 | Autophagy, negative regulation of cell death, response to stress, proteolysis |
11 | 14-3-3 protein epsilon (YWHAE) | P62258 | 2866 | 0.023 | − 1.43 | Cell cycle transition, apoptosis, membrane organization |
12 | Spermidine synthase (SRM) | P19623 | 2651 | 0.034 | 1.33 | Polyamine metabolic process, spermidine biosynthetic process |
13 | Heat shock protein beta-1 (HSPB1) | P04792 | 3078 | 0.034 | − 1.67 | Angiogenesis, anti-apoptosis, response to stress, response to unfolded protein |
14 | WD repeat-containing protein 1 (WDR1) | O75083 | 1104 | 0.035 | − 1.31 | Platelet degranulation and activation |
15 | 78 kDa glucose-regulated protein (HSPA5) | P11021 | 3366 | 0.04 | − 1.42 | Platelet degranulation and activation, anti-apoptosis, unfolded protein response, negative regulation of TGFβ receptor signaling pathway, positive regulation of protein ubiquitination |
16 | Heat shock cognate 71 kDa protein (HSPA8) | P11142 | 1158 | 0.041 | − 1.41 | Protein folding, response to stress, response to unfolded protein, cell cycle, ATP catabolic process |
17 | T-complex protein 1 subunit alpha (TCP1) | P17987 | 1355 | 0.043 | − 1.44 | Protein folding, tubulin complex assembly, cellular protein metabolic process |
18 | Annexin A5 (ANXA5) | P08758 | 2652 | 0.045 | − 1.31 | Anti-apoptosis, signal transduction |