| Literature DB >> 34012732 |
Jinsong Lin1, Shubiao Lu1, Zhijian Jiang1, Chongjing Hu1, Zhiqiao Zhang1.
Abstract
BACKGROUND: Individual mortality risk predicted curve at the individual level can provide valuable information for directing individual treatment decision. The present study attempted to explore potential post-transcriptional biological regulatory mechanism related with overall survival of lung adenocarcinoma (LUAD) patients through competitive endogenous RNA (ceRNA) network and develop two precision medicine predictive tools for predicting the individual mortality risk curves for overall survival of LUAD patients.Entities:
Keywords: Competitive endogenous RNA; Lung adenocarcinoma; Overall survival; Prognostic model; mRNA
Year: 2021 PMID: 34012732 PMCID: PMC8109009 DOI: 10.7717/peerj.11412
Source DB: PubMed Journal: PeerJ ISSN: 2167-8359 Impact factor: 2.984
The clinical features of lung adenocarcinoma patients in the model group and validation group.
| Model group ( | Validation group ( | ||
|---|---|---|---|
| Death [n(%)] | 182(36.8) | 127(54.5) | <0.001 |
| Survival time for living patients(mean ± SD, month) | 22.2(15.6,37.6) | 69.1(59.3,88.0) | <0.001 |
| Survival time for dead patients (mean ± SD, month) | 20.3(9.8,36.8) | 25.3(12.4,48.4) | 0.006 |
| Age (mean ± SD, year) | 65.3 ± 10.0 | 66.1 ± 9.9 | 0.318 |
| Male [(n)%] | 229(46.4) | 111(47.6) | 0.746 |
| AJCC Stage (IV) | 25 | 4 | <0.001 |
| AJCC Stage (III) | 80 | 13 | |
| AJCC Stage (II) | 116 | 54 | |
| AJCC Stage (I) | 273 | 162 | |
| AJCC Stage (NA) | 0 | 0 | |
| AJCC PT (T1) | 229 | NA | NA |
| AJCC PT (T0) | 265 | NA | |
| AJCC PT (NA) | 0 | NA | |
| AJCC PN (N4) | 18 | NA | NA |
| AJCC PN (N3) | 44 | NA | |
| AJCC PN (N2) | 264 | NA | |
| AJCC PN (N1) | 165 | NA | |
| AJCC PN (N0) | 3 | NA | |
| AJCC PN (NA) | 0 | NA | |
| AJCC PM (M3) | 2 | NA | NA |
| AJCC PM (M2) | 69 | NA | |
| AJCC PM (M1) | 92 | NA | |
| AJCC PM (M0) | 302 | NA | |
| AJCC PM (NA) | 11 | NA |
Note
Continuous variables were compared by t-test or Mann-Whitney U test as appropriate; Categorical variables were compared by chi-squared test or Fisher’s exact test as appropriate.
missing data
standard deviation
American Joint Committee on Cancer
Figure 1Competitive endogenous RNA network chart: the red triangles represent 22 lncRNAs; the blue triangles represent 29 miRNAs; the green circles represent 73 mRNAs.
Figure 2(A) The barplot of GO terms for prognostic mRNAs; (B) the dotplot of GO terms for prognostic mRNAs.
Figure 3(A) Chord chart of GO terms for prognostic mRNAs; (B) KEGG pathways for prognostic mRNAs.
The model information of prognostic mRNAs in univariate and multivariable Cox regression analyses.
| Univariate analysis | Multivariate analysis | ||||||
|---|---|---|---|---|---|---|---|
| Gene | HR | 95% CI | coefficient | HR | 95% CI | ||
| DNAJC27 (High/Low) | 0.594 | 0.441–0.800 | <0.001 | −0.731 | 0.482 | 0.336–0.691 | <0.001 |
| NPAS2 (High/Low) | 1.613 | 1.202-2.164 | <0.001 | 0.478 | 1.612 | 1.166–2.229 | 0.004 |
| PHKA1 (High/Low) | 1.367 | 1.020–1.832 | 0.036 | 0.394 | 1.483 | 1.032–2.131 | 0.033 |
| CDADC1 (High/Low) | 0.699 | 0.521–0.936 | 0.016 | −0.554 | 0.575 | 0.394–0.839 | 0.004 |
| PTGFRN (High/Low) | 1.356 | 1.012–1.818 | 0.042 | 0.479 | 1.615 | 1.120–2.329 | 0.010 |
| DDIT4 (High/Low) | 1.634 | 1.217–2.193 | <0.001 | 0.398 | 1.489 | 1.086–2.042 | 0.013 |
| SCAMP5 (High/Low) | 0.737 | 0.550–0.988 | 0.041 | −0.413 | 0.662 | 0.474–0.924 | 0.015 |
| SPRY2 (High/Low) | 0.714 | 0.533–0.957 | 0.024 | −0.437 | 0.646 | 0.455–0.918 | 0.015 |
| CSE1L (High/Low) | 1.342 | 1.001–1.798 | 0.049 | 0.385 | 1.470 | 1.024–2.110 | 0.037 |
| ELAVL4 (High/Low) | 0.707 | 0.527–0.950 | 0.021 | −0.394 | 0.674 | 0.496–0.918 | 0.012 |
| TRIM29 (High/Low) | 1.391 | 1.037–1.864 | 0.028 | 0.329 | 1.390 | 1.010–1.912 | 0.043 |
| LPGAT1 (High/Low) | 1.410 | 1.052–1.890 | 0.022 | 0.369 | 1.446 | 1.017–2.054 | 0.040 |
| TRPC3 (High/Low) | 0.681 | 0.506–0.915 | 0.011 | −0.328 | 0.720 | 0.525–0.988 | 0.042 |
| DCBLD2 (High/Low) | 1.346 | 1.005–1.802 | 0.046 | 0.326 | 1.385 | 1.001–1.915 | 0.049 |
Notes.
hazard ratio
confidence interval
The medians of mRNA expression values were used as cut-off values to stratify mRNA expression values into high expression group (as value 1) and low expression group (as value 0).
Figure 4The prognostic nomogram for overall survival.
Results of differential expression analysis of the enrolled mRNAs.
.
| Symbol | F | FC | logCPM | FDR | |
|---|---|---|---|---|---|
| PHKA1 | 207.115 | <0.001 | 3.252 | 4.717 | <0.001 |
| CDADC1 | 125.913 | <0.001 | 0.666 | 2.854 | <0.001 |
| LPGAT1 | 116.687 | <0.001 | 2.218 | 6.843 | <0.001 |
| PTGFRN | 104.576 | <0.001 | 2.304 | 6.604 | <0.001 |
| DNAJC27 | 95.382 | <0.001 | 0.621 | 2.815 | <0.001 |
| SCAMP5 | 66.600 | <0.001 | 2.384 | 4.159 | <0.001 |
| CSE1L | 63.349 | <0.001 | 1.694 | 6.671 | <0.001 |
| NPAS2 | 52.396 | <0.001 | 2.416 | 4.793 | <0.001 |
| TRPC3 | 44.057 | <0.001 | 0.429 | −0.488 | <0.001 |
| SPRY2 | 42.334 | <0.001 | 0.629 | 5.171 | <0.001 |
| ELAVL4 | 41.979 | <0.001 | 3.749 | −0.076 | <0.001 |
| DDIT4 | 34.794 | <0.001 | 2.249 | 7.135 | <0.001 |
| DCBLD2 | 30.157 | <0.001 | 2.262 | 7.216 | <0.001 |
| TRIM29 | 7.324 | 0.007 | 2.108 | 5.400 | 0.010 |
Figure 5(A) Survival curves in model group; (B) time-dependent receiver operating characteristic curves in model group; (C) the distribution of prognostic model score in model group; (D) the overall survival status and overall survival time in model group.
Figure 6(A) Survival curves in validation group; (B) time-dependent receiver operating characteristic curves in validation group.
Univariate and multivariable Cox regression analyses for independence assessment of prognostic model.
| Univariate analysis | Multivariate analysis | ||||||
|---|---|---|---|---|---|---|---|
| HR | 95% CI | coefficient | HR | 95% CI | |||
| Model group ( | |||||||
| Age(≥60/<60 years) | 1.003 | 0.722–1.392 | 0.987 | 0.078 | 1.082 | 0.776–1.507 | 0.643 |
| Gender (Male/Female) | 1.048 | 0.783–1.403 | 0.754 | 0.077 | 1.080 | 0.805–1.449 | 0.609 |
| AJCC stage (IV,III/II,I) | 2.599 | 1.906–3.545 | <0.001 | 0.800 | 2.225 | 1.622–3.051 | <0.001 |
| Prognostic model (High/Low) | 2.705 | 1.986–3.684 | <0.001 | 0.895 | 2.447 | 1.786–3.352 | <0.001 |
| Validation group( | |||||||
| Age(≥60/<60 years) | 0.876 | 0.595–1.289 | 0.501 | −0.271 | 0.762 | 0.512–1.136 | 0.183 |
| Gender (Male/Female) | 1.308 | 0.921–1.857 | 0.134 | 0.268 | 1.308 | 0.911–1.877 | 0.146 |
| AJCC stage (IV,III/II,I) | 0.988 | 0.517–1.888 | 0.974 | 0.354 | 1.424 | 0.738–2.750 | 0.292 |
| Prognostic model (High/Low) | 5.109 | 3.428–7.348 | <0.001 | 1.651 | 5.214 | 3.531–7.701 | <0.001 |
Notes.
the American Joint Committee on Cancer
hazard ratio
confidence interval
The median of Prognostic model scores was used as the cut-off value to stratify gastric cancer patients into high risk group and low risk group.
Figure 7Home page of Smart Cancer Survival Predictive System: (A) individual mortality risk predictive curve display page; (B) different time-point individual mortality risk prediction display page.
Figure 8Home page of Gene Survival Analysis Screen System: (A) survival curve plot display page; (B) univariate analysis table display page.