Prognostic Effect of Inflammatory Genes on Stage I–III Colorectal Cancer—Integrative Analysis of TCGA Data
Abstract
:Simple Summary
Abstract
1. Introduction
2. Methods
2.1. Data Acquisition and Preprocessing
2.2. Ethics Statement
2.3. Feature Selection
2.4. Overall Survival Prediction Based on Omic Features
3. Results
3.1. Patient Demographics
3.2. Feature Selection for Overall Survival with Lasso-Cox
3.3. Training Prediction Models for Overall Survival with Lasso-Cox
3.4. Association Analysis of Overall Survival with Multivariate Cox Proportional Hazard Regression
3.5. Gene-Gene Network and Biological Process Network
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
CRC | Colorectal |
TCGA-COREAD | The Cancer Genome Atlas-Colorectal Cancer |
Lasso-Cox | Lasso-penalized Cox proportional hazards regression |
CPH | Cox proportional hazard regression |
IMP | Integrative multispecies prediction |
LMR | Lymphocyte-to-monocyte ratio |
NLR | Neutrophil-to-lymphocyte ratio |
PLR | Platelet-to-lymphocyte ratio |
C | Clinical features |
E | Gene expression features |
M | Gene methylation features |
EM | Concatenated expression and methylation features |
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Features | Alive | Dead | p Value |
---|---|---|---|
Age | 62.9 ± 12.5 | 71.7 ± 12.6 | <0.001 |
<65 | 111 (53.1%) | 7 (18.4%) | |
≥65 | 98 (46.9%) | 31 (81.6%) | |
Continuous | 62.9 ± 12.5 | 71.7 ± 12.6 | |
Gender | 0.407 | ||
Male | 108 (51.7%) | 23 (60.5%) | |
Female | 101 (48.3%) | 15 (39.5%) | |
Overall stage | 0.201 | ||
Stage 1, 2 | 136 (65.1%) | 20 (52.6%) | |
Stage 3 | 73 (34.9%) | 18 (47.4%) | |
Stage 1 | 46 (22.0%) | 2 (5.3%) | |
Stage 2 | 90 (43.1%) | 18 (47.4%) | |
Stage 3 | 73 (34.9%) | 18 (47.4%) | |
T stage | 0.046 | ||
T1, T2 | 50 (23.9%) | 3 (7.9%) | |
T3, T4 | 159 (76.1%) | 35 (92.1%) | |
T1 | 8 (3.8%) | 1 (2.6%) | |
T2 | 42 (20.1%) | 2 (5.3%) | |
T3 | 146 (69.9%) | 32 (84.2%) | |
T4 | 13 (6.2%) | 3 (7.9%) | |
N stage | 0.113 | ||
LN negative | 136 (65.1%) | 19 (50.0%) | |
LN positive | 73 (34.9%) | 19 (50.0%) | |
N0 | 136 (65.1%) | 19 (50.0%) | |
N1 | 49 (23.4%) | 9 (23.7%) | |
N2 | 24 (11.5%) | 10 (26.3%) | |
Tumor location | 1 | ||
Right colon | 102 (50.2%) | 17 (48.6%) | |
Left colon | 101 (49.8%) | 18 (51.4%) | |
Venous invasion | 0.916 | ||
Negative | 147 (80.8%) | 25 (78.1%) | |
Positive | 35 (19.2%) | 7 (21.9%) | |
Lymphatic invasion | 0.887 | ||
Negative | 140 (75.7%) | 24 (72.7%) | |
Positive | 45 (24.3%) | 9 (27.3%) | |
Follow up duration (months) | 38.54 ± 31.26 | 39.97 ± 22.79 | 0.739 |
Features Used | Min. | 1st Qu. | Median | Mean | 3rd Qu. | Max. |
---|---|---|---|---|---|---|
Clinical features | 0.318 | 0.648 | 0.726 | 0.706 | 0.791 | 0.921 |
Expression features | 0.449 | 0.614 | 0.691 | 0.688 | 0.774 | 0.899 |
Methylation features | 0.447 | 0.580 | 0.686 | 0.683 | 0.772 | 0.899 |
Expression features + Methylation features | 0.337 | 0.647 | 0.727 | 0.715 | 0.826 | 0.884 |
Clinical features + Expression features | 0.438 | 0.609 | 0.667 | 0.673 | 0.761 | 0.832 |
Clinical features + Methylation features | 0.333 | 0.628 | 0.704 | 0.682 | 0.757 | 0.866 |
Clinical features + Expression features + Methylation features | 0.326 | 0.655 | 0.756 | 0.708 | 0.818 | 0.883 |
Features | Hazard Ratio (HR) | 95% CI, Lower | 95% CI, Upper | Z Value | Adjusted p Value |
---|---|---|---|---|---|
Age | 1.697 | 0.609 | 4.733 | 1.011 | 0.312 |
N stage | 2.942 | 1.253 | 6.912 | 2.477 | 0.013 |
T stage | 0.919 | 0.237 | 3.557 | −0.122 | 0.903 |
Gender | 0.910 | 0.390 | 2.121 | −0.219 | 0.827 |
CEP250 (methylation) | 0.592 | 0.364 | 0.963 | −2.110 | 0.035 |
DEFA5 (expression) | 0.786 | 0.462 | 1.337 | −0.888 | 0.374 |
MAZ (methylation) | 0.967 | 0.809 | 1.156 | −0.369 | 0.712 |
NINJ1 (methylation) | 1.339 | 0.910 | 1.968 | 1.482 | 0.138 |
NLRP14 (expression) | 0.797 | 0.525 | 1.211 | −1.063 | 0.288 |
PPARGC1A (expression) | 0.808 | 0.636 | 1.027 | −1.744 | 0.081 |
PRG4 (expression) | 1.256 | 0.871 | 1.811 | 1.219 | 0.223 |
PTGES (expression) | 1.399 | 0.937 | 2.087 | 1.644 | 0.100 |
RAB21 (methylation) | 1.556 | 1.172 | 2.065 | 3.060 | 0.002 |
TERF2IP (expression) | 1.452 | 0.893 | 2.360 | 1.502 | 0.133 |
TMEM184A (expression) | 1.251 | 0.819 | 1.911 | 1.038 | 0.299 |
TNFRSF18 (methylation) | 1.489 | 0.783 | 2.829 | 1.214 | 0.225 |
TNFSF12 (methylation) | 1.132 | 0.801 | 1.600 | 0.704 | 0.481 |
TNPO3 (methylation) | 1.465 | 1.092 | 1.967 | 2.543 | 0.011 |
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Choe, E.K.; Lee, S.; Kim, S.Y.; Shivakumar, M.; Park, K.J.; Chai, Y.J.; Kim, D. Prognostic Effect of Inflammatory Genes on Stage I–III Colorectal Cancer—Integrative Analysis of TCGA Data. Cancers 2021, 13, 751. https://doi.org/10.3390/cancers13040751
Choe EK, Lee S, Kim SY, Shivakumar M, Park KJ, Chai YJ, Kim D. Prognostic Effect of Inflammatory Genes on Stage I–III Colorectal Cancer—Integrative Analysis of TCGA Data. Cancers. 2021; 13(4):751. https://doi.org/10.3390/cancers13040751
Chicago/Turabian StyleChoe, Eun Kyung, Sangwoo Lee, So Yeon Kim, Manu Shivakumar, Kyu Joo Park, Young Jun Chai, and Dokyoon Kim. 2021. "Prognostic Effect of Inflammatory Genes on Stage I–III Colorectal Cancer—Integrative Analysis of TCGA Data" Cancers 13, no. 4: 751. https://doi.org/10.3390/cancers13040751