Introduction
Materials and methods
Data acquisition and processing
Variable | Number of samples |
---|---|
Age at diagnosis(< 60/ ≥ 60/NA) | 418/379/1 |
Gender (male/female) | 608/190 |
Grade(G1/G2/G3/G4/NA) | 63/311/124/7/291 |
Stage(I/II/III/IV/NA) | 27/74/82/269/76 |
T (T0/T1/T2/T3/T4/NA) | 1/49/140/101/174/63 |
M(M0/M1/NA) | 453/8/337 |
N(N0/N1/N2/N3/NA) | 273/100/304/20/101 |
HPV16(negative/positive/NA) | 128/237/433 |
Variable | Number of samples |
---|---|
Age at diagnosis (< 60/ ≥ 60) | 50/47 |
Gender(Male/Female) | 66/31 |
Stage(I-II/III-IV) | 41/56 |
HPV16(negative) | 97 |
Variable | Healthy donor | HNSCC |
---|---|---|
Age (< 60/ ≥ 60) | 3/2 | 13/13 |
Gender(Male/Female) | 3/2 | 20/6 |
Stage(I-II/III-IV) | – | 12/14 |
HPV16(negative) | – | 18/8 |
Unsupervised clustering of hypoxia-related genes
Immune cell infiltration and function
Biofunction prediction
Hypoxia scoring model
Potential sensitive multiple therapeutic predictions
Identification of key genes related to hypoxia
Cell culture and retroviral infection
Western blotting
CCK-8 assay
Transwell assays
Statistical analyses
Results
Genetic variation in hypoxia-related genes among HNSCC patients
Stratification of HNSCC based on hypoxia-related gene sets
Immune characteristics and biological behaviors of the three hypoxia clusters
Stratification of HNSCC based on differentially expressed genes
Hypoxia score combined with tumor mutation burden and stromal/immune/Estimate Scores could further refine the prognosis of HNSCC patients
Hypoxia scores have a great potential to predict the efficacy of different therapies
The key gene identified based on hypoxia scores
Single-cell sequencing data revealed the mechanism of different immune cells in hypoxia
Cell–cell communication in HNSCC
Prognostic role of HLA-DPA1 and CD4 in HNSCC
Cell type | Gene markers | HLA-DPA1 | CD4 | ||||||
---|---|---|---|---|---|---|---|---|---|
None | Purity | None | Purity | ||||||
Cor | p-value | cor | p-value | Cor | p-value | Cor | p-value | ||
CD8 + T | CD8A | 8.06E-01 | 0.00E + 00 | −2.77E-01 | 4.03E-10 | 7.48E-01 | 1.75E-89 | −2.77E-01 | 4.03E-10 |
CD8B | 7.65E-01 | 1.45E−101 | −2.42E-01 | 5.06E-08 | 7.15E-01 | 2.38E-78 | −2.42E-01 | 5.06E-08 | |
T cell (general) | CD3D | 8.01E-01 | 0.00E + 00 | −2.98E-01 | 1.35E-11 | 7.46E-01 | 1.47E-88 | −2.98E-01 | 1.35E-11 |
CD3E | 8.47E-01 | 9.59E−145 | −2.99E-01 | 1.17E-11 | 8.43E-01 | 2.18E-134 | −2.99E-01 | 1.17E-11 | |
CD2 | 8.50E-01 | 0.00E + 00 | −2.85E-01 | 1.15E-10 | 8.36E-01 | 3.54E-130 | −2.85E-01 | 1.15E-10 | |
B cell | CD19 | 4.77E-01 | 5.74E−31 | −2.61E-01 | 4.33E-09 | 5.05E-01 | 2.74E-33 | −2.61E-01 | 4.33E-09 |
CD79A | 4.71E-01 | 3.47E−30 | −2.28E-01 | 3.05E-07 | 5.12E-01 | 2.50E-34 | −2.28E-01 | 3.05E-07 | |
Monocyte | CD86 | 7.73E-01 | 0.00E + 00 | −2.95E-01 | 2.26E-11 | 8.45E-01 | 2.22E-135 | −2.95E-01 | 2.26E-11 |
CD115 (CSF1R) | 8.33E-01 | 6.76E−136 | −3.04E-01 | 4.98E-12 | 9.39E-01 | 5.83E-230 | −3.04E-01 | 4.98E-12 | |
TAM | CCL2 | 5.50E-01 | 0.00E + 00 | −2.58E-01 | 5.98E-09 | 6.13E-01 | 2.64E-52 | −2.58E-01 | 5.98E-09 |
CD68 | 4.52E-01 | 0.00E + 00 | −1.72E-01 | 1.24E-04 | 5.68E-01 | 1.75E-43 | −1.72E-01 | 1.24E-04 | |
IL10 | 5.57E-01 | 7.92E−44 | −3.13E-01 | 1.21E-12 | 6.28E-01 | 1.74E-55 | −3.13E-01 | 1.21E-12 | |
M1 macrophage | INOS (NOS2) | 2.55E-01 | 3.57E−09 | 7.08E-02 | 1.16E-01 | 2.96E-01 | 2.09E-11 | 7.08E-02 | 1.16E-01 |
IRF5 | 3.14E-01 | 3.02E−13 | −1.43E-03 | 9.75E-01 | 3.82E-01 | 1.44E-18 | −1.43E-03 | 9.75E-01 | |
M2 macrophage | COX2 (PTGS2) | -1.53E-01 | 4.45E−04 | 9.98E-02 | 2.67E-02 | -1.55E-01 | 5.32E-04 | 9.98E-02 | 2.67E-02 |
CD163 | 6.89E-01 | 0.00E + 00 | −2.86E-01 | 1.02E-10 | 8.07E-01 | 2.37E-114 | −2.86E-01 | 1.02E-10 | |
VSIG4 | 6.22E-01 | 0.00E + 00 | −2.57E-01 | 7.42E-09 | 7.53E-01 | 3.02E-91 | −2.57E-01 | 7.42E-09 | |
MS4A4A | 7.38E-01 | 5.15E−91 | −2.87E-01 | 8.35E-11 | 8.38E-01 | 1.73E-131 | −2.87E-01 | 8.35E-11 | |
Neutr-ophils | CD66b (CEACAM8) | 5.92E-02 | 1.77E−01 | 3.42E-02 | 4.48E-01 | 4.51E-02 | 3.18E-01 | 3.42E-02 | 4.48E-01 |
CD11b (ITGAM) | 6.00E-01 | 2.39E−52 | −1.37E-01 | 2.27E-03 | 7.20E-01 | 7.13E-80 | −1.37E-01 | 2.27E-03 | |
CCR7 | 6.52E-01 | 1.71E−64 | −3.22E-01 | 2.23E-13 | 7.38E-01 | 9.46E-86 | −3.22E-01 | 2.23E-13 | |
NK cell | KIR2DL1 | 3.81E-01 | 1.69E−19 | −9.34E-02 | 3.81E-02 | 3.44E-01 | 4.23E-15 | −9.34E-02 | 3.81E-02 |
KIR2DL3 | 5.10E-01 | 6.99E−36 | −1.36E-01 | 2.56E-03 | 4.69E-01 | 2.57E-28 | −1.36E-01 | 2.56E-03 | |
KIR2DL4 | 6.02E-01 | 7.92E−53 | −1.83E-01 | 4.30E-05 | 4.95E-01 | 7.06E-32 | −1.83E-01 | 4.30E-05 | |
KIR3DL1 | 4.47E-01 | 4.78E−27 | −1.44E-01 | 1.35E-03 | 4.27E-01 | 2.70E-23 | −1.44E-01 | 1.35E-03 | |
KIR3DL2 | 5.74E-01 | 4.40E−47 | −1.47E-01 | 1.05E-03 | 5.56E-01 | 2.63E-41 | −1.47E-01 | 1.05E-03 | |
KIR3DL3 | 2.33E-01 | 7.00E−08 | −8.59E-02 | 5.68E-02 | 2.05E-01 | 4.56E-06 | −8.59E-02 | 5.68E-02 | |
KIR2DS4 | 3.47E-01 | 2.92E−16 | −1.48E-01 | 9.93E-04 | 3.32E-01 | 4.09E-14 | −1.48E-01 | 9.93E-04 | |
Dend-ritic cell | HLA-DPB1 | 9.57E-01 | 0.00E + 00 | −3.02E-01 | 7.78E-12 | 8.70E-01 | 1.09E-152 | −3.02E-01 | 7.78E-12 |
HLA-DQB1 | 8.14E-01 | 6.55E−125 | −2.28E-01 | 3.28E-07 | 7.03E-01 | 1.07E-74 | −2.28E-01 | 3.28E-07 | |
HLA-DRA | 9.74E-01 | 0.00E + 00 | −2.99E-01 | 1.16E-11 | 8.51E-01 | 1.33E-139 | −2.99E-01 | 1.16E-11 | |
BDCA-1 | 5.37E-01 | 2.59E−40 | −2.57E-01 | 7.19E-09 | 6.25E-01 | 1.07E-54 | −2.57E-01 | 7.19E-09 | |
BDCA-4 | 4.59E-01 | 1.61E−28 | −2.07E-01 | 3.38E-06 | 5.65E-01 | 6.16E-43 | −2.07E-01 | 3.38E-06 | |
CD11c | 6.45E-01 | 1.01E−62 | −2.83E-01 | 1.53E-10 | 7.89E-01 | 7.01E-106 | −2.83E-01 | 1.53E-10 | |
T-bet (TBX21) | 7.88E-01 | 9.07E−112 | −2.44E-01 | 4.20E-08 | 7.68E-01 | 2.85E-97 | −2.44E-01 | 4.20E-08 | |
Th1 | STAT4 | 6.52E-01 | 0.00E + 00 | −2.61E-01 | 3.96E-09 | 6.94E-01 | 6.30E-72 | −2.61E-01 | 3.96E-09 |
STAT1 | 6.26E-01 | 0.00E + 00 | −2.40E-01 | 7.06E-08 | 5.29E-01 | 5.97E-37 | −2.40E-01 | 7.06E-08 | |
IFN-y(IFNG) | 7.09E-01 | 5.81E−81 | −2.34E-01 | 1.49E-07 | 5.79E-01 | 2.19E-45 | −2.34E-01 | 1.49E-07 | |
TNF-a(TNF) | 2.28E-01 | 1.47E−07 | −1.27E-01 | 4.90E-03 | 2.26E-01 | 4.19E-07 | −1.27E-01 | 4.90E-03 | |
Th2 | GATA3 | 4.56E-01 | 3.72E−28 | −2.27E-01 | 3.63E-07 | 4.93E-01 | 1.61E-31 | −2.27E-01 | 3.63E-07 |
STAT5A | 6.20E-01 | 8.53E−57 | −1.32E-01 | 3.28E-03 | 6.43E-01 | 9.08E-59 | −1.32E-01 | 3.28E-03 | |
STAT6 | 2.90E-01 | 1.73E−11 | 6.90E-02 | 1.26E-01 | 3.25E-01 | 1.31E-13 | 6.90E-02 | 1.26E-01 | |
IL13 | 4.10E-01 | 1.52E−22 | −1.54E-01 | 5.78E-04 | 4.22E-01 | 1.06E-22 | −1.54E-01 | 5.78E-04 | |
Tfh | BCL6 | 8.87E-02 | 4.28E−02 | 1.75E-01 | 8.98E-05 | 1.69E-01 | 1.57E-04 | 1.75E-01 | 8.98E-05 |
IL21 | 5.20E-01 | 2.03E−37 | −1.75E-01 | 9.02E-05 | 5.12E-01 | 2.50E-34 | −1.75E-01 | 9.02E-05 | |
Th17 | STAT3 | 3.84E-01 | 0.00E + 00 | −1.69E-02 | 7.08E-01 | 4.09E-01 | 2.82E-21 | −1.69E-02 | 7.08E-01 |
IL17A | 2.85E-01 | 3.45E−11 | −1.02E-01 | 2.40E-02 | 2.74E-01 | 6.59E-10 | −1.02E-01 | 2.40E-02 | |
Treg | FOXP3 | 7.93E-01 | 0.00E + 00 | −2.53E-01 | 1.18E-08 | 8.70E-01 | 9.39E-153 | −2.53E-01 | 1.18E-08 |
CCR8 | 6.88E-01 | 2.64E−74 | −2.34E-01 | 1.39E-07 | 7.89E-01 | 4.56E-106 | −2.34E-01 | 1.39E-07 | |
STAT5B | 3.76E-01 | 6.17E−19 | −5.12E-02 | 2.56E-01 | 4.91E-01 | 2.65E-31 | −5.12E-02 | 2.56E-01 | |
TGFb(TGFb1) | 4.60E-02 | 2.95E−01 | −1.42E-01 | 1.55E-03 | 1.36E-01 | 2.39E-03 | −1.42E-01 | 1.55E-03 | |
T-cell -exhau-stion | PD-1(PDCD1) | 8.20E-01 | 7.03E−128 | −2.68E-01 | 1.57E-09 | 7.74E-01 | 1.45E-99 | −2.68E-01 | 1.57E-09 |
CTLA4 | 7.66E-01 | 0.00E + 00 | −3.10E-01 | 2.04E-12 | 7.69E-01 | 1.14E-97 | −3.10E-01 | 2.04E-12 | |
LAG3 | 7.67E-01 | 2.04E−102 | −2.37E-01 | 9.98E-08 | 6.97E-01 | 7.88E-73 | −2.37E-01 | 9.98E-08 | |
TIM-3(HAVCR2) | 8.68E-01 | 0.00E + 00 | −2.77E-01 | 3.81E-10 | 9.26E-01 | 2.09E-209 | −2.77E-01 | 3.81E-10 | |
GZMB | 7.22E-01 | 0.00E + 00 | −2.64E-01 | 2.68E-09 | 6.14E-01 | 2.30E-52 | −2.64E-01 | 2.68E-09 |
Cancer | Symbol | Cell type | Cor | p_value | Fdr |
---|---|---|---|---|---|
HNSC | CD4 | Bcell | 0.125229401 | 0.002840681 | 0.00709747 |
HNSC | CD4 | CD4_T | 0.498597147 | 6.63574E-37 | 2.34323E-35 |
HNSC | CD4 | CD4_naive | −0.32641244 | 1.61664E-15 | 2.27551E-13 |
HNSC | CD4 | CD8_T | 0.487711864 | 3.70562E-35 | 2.41381E-33 |
HNSC | CD4 | CD8_naive | −0.27974378 | 1.23245E-11 | 3.86398E-10 |
HNSC | CD4 | Central_memory | 0.399107546 | 4.69625E-23 | 1.75049E-21 |
HNSC | CD4 | Cytotoxic | 0.648867218 | 6.05612E-69 | 6.66107E-67 |
HNSC | CD4 | DC | 0.264792464 | 1.55096E-10 | 1.81922E-09 |
HNSC | CD4 | Effector_memory | −0.348009036 | 1.47439E-17 | 3.6235E-16 |
HNSC | CD4 | Exhausted | 0.430230051 | 6.61951E-27 | 3.14239E-25 |
HNSC | CD4 | Gamma_delta | 0.350506267 | 8.36139E-18 | 1.3932E-16 |
HNSC | CD4 | InfiltrationScore | 0.774932647 | 1.8103E-114 | 6.1759E-112 |
HNSC | CD4 | MAIT | −0.079904273 | 0.057456885 | 0.102199733 |
HNSC | CD4 | Macrophage | 0.623132464 | 3.43057E-62 | 7.75849E-60 |
HNSC | CD4 | Monocyte | 0.026849971 | 0.52380974 | 0.648854849 |
HNSC | CD4 | NK | 0.452353693 | 6.74773E-30 | 3.80443E-28 |
HNSC | CD4 | NKT | −0.069342829 | 0.099341311 | 0.161500841 |
HNSC | CD4 | Neutrophil | −0.734956861 | 3.26494E-97 | 7.73137E-95 |
HNSC | CD4 | Tfh | 0.61809823 | 6.07528E-61 | 5.07399E-59 |
HNSC | CD4 | Th1 | 0.400553951 | 3.17398E-23 | 1.31996E-21 |
HNSC | CD4 | Th17 | −0.522771785 | 5.12345E-41 | 7.99417E-39 |
HNSC | CD4 | Th2 | 0.151716151 | 0.000291823 | 0.001462605 |
HNSC | CD4 | Tr1 | 0.526495547 | 1.11241E-41 | 2.11779E-39 |
HNSC | CD4 | iTreg | 0.578673885 | 6.65288E-52 | 2.15983E-49 |
HNSC | CD4 | nTreg | 0.132102751 | 0.001634437 | 0.004873403 |
HNSC | HLA-DPA1 | Bcell | 0.160458983 | 0.000126143 | 0.000439536 |
HNSC | HLA-DPA1 | CD4_T | 0.390194718 | 5.0338E-22 | 5.91479E-21 |
HNSC | HLA-DPA1 | CD4_naive | −0.341193739 | 6.75694E-17 | 1.51115E-14 |
HNSC | HLA-DPA1 | CD8_T | 0.571758553 | 1.92463E-50 | 2.54861E-48 |
HNSC | HLA-DPA1 | CD8_naive | −0.353117464 | 4.59558E-18 | 6.00057E-16 |
HNSC | HLA-DPA1 | Central_memory | 0.317720549 | 9.66095E-15 | 1.05282E-13 |
HNSC | HLA-DPA1 | Cytotoxic | 0.718927306 | 3.78606E-91 | 9.64631E-89 |
HNSC | HLA-DPA1 | DC | 0.170909511 | 0.000043664 | 0.000157248 |
HNSC | HLA-DPA1 | Effector_memory | −0.142157787 | 0.000694338 | 0.001711443 |
HNSC | HLA-DPA1 | Exhausted | 0.527673099 | 6.83588E-42 | 8.82004E-40 |
HNSC | HLA-DPA1 | Gamma_delta | 0.399847288 | 3.84448E-23 | 1.39931E-21 |
HNSC | HLA-DPA1 | InfiltrationScore | 0.6560327 | 6.07356E-71 | 6.57251E-69 |
HNSC | HLA-DPA1 | MAIT | −0.069344284 | 0.099334199 | 0.161528417 |
HNSC | HLA-DPA1 | Macrophage | 0.482428439 | 2.47987E-34 | 1.81509E-32 |
HNSC | HLA-DPA1 | Monocyte | −0.170950179 | 0.000043478 | 0.000248193 |
HNSC | HLA-DPA1 | NK | 0.545950055 | 2.77657E-45 | 4.17066E-43 |
HNSC | HLA-DPA1 | NKT | −0.11742411 | 0.005156123 | 0.012552302 |
HNSC | HLA-DPA1 | Neutrophil | −0.72886484 | 7.40981E-95 | 1.60371E-92 |
HNSC | HLA-DPA1 | Tfh | 0.636744419 | 1.10534E-65 | 1.08002E-63 |
HNSC | HLA-DPA1 | Th1 | 0.549856923 | 4.91135E-46 | 6.21734E-44 |
HNSC | HLA-DPA1 | Th17 | −0.493278817 | 4.82249E-36 | 4.78163E-34 |
HNSC | HLA-DPA1 | Th2 | 0.188362098 | 6.42744E-06 | 0.000064815 |
HNSC | HLA-DPA1 | Tr1 | 0.327139515 | 1.38843E-15 | 1.57711E-14 |
HNSC | HLA-DPA1 | iTreg | 0.493931466 | 3.78772E-36 | 3.23048E-34 |
HNSC | HLA-DPA1 | nTreg | 0.127127138 | 0.002444997 | 0.006899699 |