Single-Cell Deconvolution of Head and Neck Squamous Cell Carcinoma
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. Overview of Deconvolution Approach
2.2. CIBERSORTx Analysis with scRNA-seq Reference for Nine Major Cell Types
2.3. CIBERSORTx Analysis with T-Cell Subtypes/Subpopulations
2.4. MuSiC Deconvolution Based on T-Cell Subtypes/Subpopulations
2.5. CIBERSORTx Analysis of Gene Expression of Regulatory T-Cells
3. Discussion
4. Methods
4.1. Bulk RNA-Seq Data and Clinical Information of HNSCC Tumors from TCGA
4.2. Single-Cell RNA-seq Data of HNSCC Tumors
4.3. CIBERSORTx Deconvolution Analysis
4.4. MuSiC Deconvolution Analysis
4.5. Single-Cell RNA-seq Data of HNSCC Tumors
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Variables | CIBERSORTx | MuSiC | ||||
---|---|---|---|---|---|---|
HR | 95% CI | p | HR | 95% CI | p | |
Cell type prop. | ||||||
T-cell low (ref) | 1.00 | 1.00 | ||||
T-cell high | 0.63 | 0.47–0.83 | 0.001 | 0.71 | 0.53–0.93 | 0.014 |
Stage | ||||||
Stage I (ref) | 1.00 | 1.00 | ||||
Stage II | 1.50 | 0.58–3.90 | 0.404 | 1.49 | 0.57–3.87 | 0.415 |
Stage III | 1.83 | 0.71–4.71 | 0.21 | 1.80 | 0.70–4.63 | 0.224 |
Stage IVA | 2.53 | 1.03–6.21 | 0.043 | 2.45 | 1.00–6.04 | 0.051 |
Stage IVB | 5.53 | 1.66–18.39 | 0.005 | 5.56 | 1.67–18.51 | 0.005 |
Stage IVC | 17.61 | 1.92–161.32 | 0.011 | 18.38 | 2.00–168.47 | 0.01 |
Not reported | 2.21 | 0.84–5.81 | 0.107 | 2.05 | 0.78–5.38 | 0.145 |
Race | ||||||
White (ref) | 1.00 | 1.00 | ||||
Black | 1.39 | 0.86–2.26 | 0.18 | 1.36 | 0.84–2.21 | 0.212 |
Hispanic | 1.53 | 0.85–2.75 | 0.159 | 1.46 | 0.81–2.63 | 0.21 |
Other | 1.11 | 0.56–2.19 | 0.761 | 1.18 | 0.60–2.33 | 0.631 |
Smoke | ||||||
Never (ref) | 1.00 | 1.00 | ||||
Ever | 0.88 | 0.63–1.22 | 0.437 | 0.88 | 0.63–1.22 | 0.446 |
Age | 1.02 | 1.00–1.03 | 0.007 | 1.02 | 1.01–1.03 | 0.004 |
Variables | CIBERSORTx | MuSiC | ||||
---|---|---|---|---|---|---|
HR | 95% CI | p | HR | 95% CI | p | |
Cell type prop. | ||||||
B-cell low (ref) | 1.00 | 1.00 | ||||
B-cell high | 0.59 | 0.45–0.79 | 3 × 10−4 | 0.69 | 0.44–1.11 | 0.126 |
Stage | ||||||
Stage I (ref) | 1.00 | 1.00 | ||||
Stage II | 1.57 | 0.60–4.08 | 0.353 | 1.67 | 0.64–4.34 | 0.293 |
Stage III | 1.93 | 0.75–4.96 | 0.173 | 1.94 | 0.76–4.99 | 0.168 |
Stage IVA | 2.71 | 1.11–6.65 | 0.029 | 2.72 | 1.11–6.66 | 0.029 |
Stage IVB | 5.95 | 1.79–19.74 | 0.004 | 6.75 | 2.03–22.44 | 0.002 |
Stage IVC | 27.77 | 3.03–254.86 | 0.003 | 21.37 | 2.34–194.94 | 0.007 |
Not reported | 2.34 | 0.89–6.14 | 0.085 | 2.18 | 0.83–5.73 | 0.114 |
Race | ||||||
White (ref) | 1.00 | 1.00 | ||||
Black | 1.57 | 0.97–2.55 | 0.069 | 1.46 | 0.9–2.37 | 0.127 |
Hispanic | 1.54 | 0.86–2.78 | 0.15 | 1.52 | 0.84–2.74 | 0.163 |
Other | 1.08 | 0.55–2.12 | 0.834 | 1.09 | 0.56–2.16 | 0.795 |
Smoke | ||||||
Never (ref) | 1.00 | 1.00 | ||||
Ever | 0.85 | 0.61–1.19 | 0.343 | 0.88 | 0.63–1.22 | 0.432 |
Age | 1.02 | 1.01–1.03 | 0.003 | 1.02 | 1.01–1.03 | 0.006 |
Variables | CIBERSORTx | MuSiC | ||||
---|---|---|---|---|---|---|
HR | 95% CI | p | HR | 95% CI | p | |
Cell type prop. | ||||||
Treg low (ref) | 1.00 | 1.00 | ||||
Treg high | 0.61 | 0.46–0.80 | 4 × 10−4 | 0.70 | 0.52–0.95 | 0.021 |
Stage | ||||||
Stage I (ref) | 1.00 | 1.00 | ||||
Stage II | 1.75 | 0.67–4.54 | 0.252 | 1.54 | 0.59–4.01 | 0.372 |
Stage III | 2.05 | 0.79–5.26 | 0.138 | 1.86 | 0.72–4.79 | 0.196 |
Stage IVA | 2.87 | 1.17–7.05 | 0.022 | 2.59 | 1.06–6.36 | 0.038 |
Stage IVB | 6.21 | 1.87–20.63 | 0.003 | 5.87 | 1.77–19.46 | 0.004 |
Stage IVC | 31.03 | 3.36–286.33 | 0.002 | 18.37 | 2.01–168.11 | 0.01 |
Not reported | 2.51 | 0.95–6.61 | 0.064 | 2.05 | 0.78–5.37 | 0.146 |
Race | ||||||
White (ref) | 1.00 | 1.00 | ||||
Black | 1.46 | 0.90–2.37 | 0.126 | 1.52 | 0.94–2.48 | 0.089 |
Hispanic | 1.48 | 0.82–2.67 | 0.191 | 1.55 | 0.86–2.79 | 0.148 |
Other | 1.06 | 0.54–2.10 | 0.862 | 1.09 | 0.56–2.15 | 0.796 |
Smoke | ||||||
Never (ref) | 1.00 | 1.00 | ||||
Ever | 0.87 | 0.62–1.21 | 0.409 | 0.85 | 0.61–1.18 | 0.335 |
Age | 1.02 | 1.01–1.03 | 0.006 | 1.02 | 1.01–1.03 | 0.005 |
Variables | Bulk RNAseq | CIBERSORTx—Treg | ||||
---|---|---|---|---|---|---|
HR | 95% CI | p | HR | 95% CI | p | |
Cell type prop. | ||||||
TNFRSF4 low (ref) | 1.00 | 1.00 | ||||
TNFRSF4 high | 0.57 | 0.43–0.75 | 8 × 10−5 | 0.59 | 0.46–0.75 | 2 × 10−5 |
Stage | ||||||
Stage I (ref) | 1.00 | 1.00 | ||||
Stage II | 2.31 | 0.88–6.02 | 0.088 | 2.03 | 0.88–4.70 | 0.097 |
Stage III | 1.54 | 0.59–4.00 | 0.376 | 1.60 | 0.72–3.56 | 0.249 |
Stage IVA | 1.78 | 0.69–4.59 | 0.232 | 1.87 | 0.84–4.17 | 0.128 |
Stage IVB | 2.65 | 1.08–6.52 | 0.033 | 2.64 | 1.23–5.65 | 0.013 |
Stage IVC | 4.79 | 1.44–15.92 | 0.011 | 5.28 | 1.76–15.84 | 0.003 |
Not reported | 16.43 | 1.80–150.11 | 0.013 | 22.36 | 2.59–193.19 | 0.005 |
Race | ||||||
White (ref) | 1.00 | 1.00 | ||||
Black | 1.55 | 0.96–2.49 | 0.073 | 1.55 | 1.00–2.41 | 0.05 |
Hispanic | 1.55 | 0.88–2.74 | 0.128 | 1.64 | 0.98–2.73 | 0.058 |
Other | 1.10 | 0.55–2.17 | 0.792 | 1.21 | 0.69–2.13 | 0.51 |
Smoke | ||||||
Never (ref) | 1.00 | 1.00 | ||||
Ever | 0.83 | 0.59–1.15 | 0.258 | 0.74 | 0.55–0.98 | 0.036 |
Age | 1.02 | 1.00–1.03 | 0.009 | 1.02 | 1.01–1.03 | 0.002 |
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Qi, Z.; Liu, Y.; Mints, M.; Mullins, R.; Sample, R.; Law, T.; Barrett, T.; Mazul, A.L.; Jackson, R.S.; Kang, S.Y.; et al. Single-Cell Deconvolution of Head and Neck Squamous Cell Carcinoma. Cancers 2021, 13, 1230. https://doi.org/10.3390/cancers13061230
Qi Z, Liu Y, Mints M, Mullins R, Sample R, Law T, Barrett T, Mazul AL, Jackson RS, Kang SY, et al. Single-Cell Deconvolution of Head and Neck Squamous Cell Carcinoma. Cancers. 2021; 13(6):1230. https://doi.org/10.3390/cancers13061230
Chicago/Turabian StyleQi, Zongtai, Yating Liu, Michael Mints, Riley Mullins, Reilly Sample, Travis Law, Thomas Barrett, Angela L. Mazul, Ryan S. Jackson, Stephen Y. Kang, and et al. 2021. "Single-Cell Deconvolution of Head and Neck Squamous Cell Carcinoma" Cancers 13, no. 6: 1230. https://doi.org/10.3390/cancers13061230