The Gasdermin E Gene Has Potential as a Pan-Cancer Biomarker, While Discriminating between Different Tumor Types
Abstract
:1. Introduction
2. Results
2.1. GSDME Differential Methylation Across 14 Tumor Types
2.2. GSDME Methylation as a Pan-Cancer Detection Biomarker
2.2.1. Initial Predictor Combination Selection
2.2.2. Individual Dataset Analysis
2.2.3. Final Model and Validation
2.3. GSDME Methylation as a Tumor-Specific Biomarker
2.4. The Relation of GSDME Methylation to RNA-seq Expression and Clinicopathological Parameters
3. Discussion
4. Materials and Methods
4.1. Datasets and Study Population
4.2. Statistical Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Dataset Name (TCGA Abbreviation) | Number of NT | Number of TP | Total |
---|---|---|---|
Bladder urothelial carcinoma (BLCA) | 21 | 418 | 439 |
Breast carcinoma (BRCA) | 96 | 791 | 887 |
Esophageal carcinoma (ESCA) | 16 | 185 | 201 |
Head and Neck squamous cell carcinoma (HNSC) | 50 | 528 | 578 |
Kidney renal clear cell carcinoma (KIRC) | 160 | 324 | 484 |
Kidney renal papillary cell carcinoma (KIRP) | 45 | 275 | 320 |
Liver hepatocellular carcinoma (LIHC) | 50 | 377 | 427 |
Lung adenocarcinoma (LUAD) | 32 | 473 | 505 |
Lung squamous cell carcinoma (LUSC) | 42 | 370 | 412 |
Pancreatic adenocarcinoma (PAAD) | 10 | 184 | 194 |
Prostate adenocarcinoma (PRAD) | 50 | 502 | 552 |
Thyroid carcinoma (THCA) | 56 | 507 | 563 |
Uterine Corpus Endometrial Carcinoma (UCEC) | 46 | 438 | 484 |
Colorectal carcinoma (CRC) | 45 | 411 | 456 |
Total | 719 | 5783 | 6502 |
Probe Abbreviation | Probe Name (Illumina) | Genomic Coordinate * | Location | Chromosome |
---|---|---|---|---|
Probe 1 | CpG17790129 | 24738572 | Gene body | 7 |
Probe 2 | CpG14205998 | 24748668 | Gene body | 7 |
Probe 3 | CpG04317854 | 24762562 | Gene body | 7 |
Probe 4 | CpG12922093 | 24767644 | Gene body | 7 |
Probe 5 | CpG17569154 | 24781545 | Gene body | 7 |
Probe 6 | CpG19260663 | 24791121 | Gene body | 7 |
Probe 7 | CpG09333471 | 24796355 | Putative Promoter | 7 |
Probe 8 | CpG00473134 | 24796494 | Putative Promoter | 7 |
Probe 9 | CpG03995857 | 24796553 | Putative Promoter | 7 |
Probe 10 | CpG07320646 | 24796981 | Putative Promoter | 7 |
Probe 11 | CpG07293520 | 24797192 | Putative Promoter | 7 |
Probe 12 | CpG04770504 | 24797363 | Putative Promoter | 7 |
Probe 13 | CpG24805239 | 24797486 | Putative Promoter | 7 |
Probe 14 | CpG01733570 | 24797656 | Putative Promoter | 7 |
Probe 15 | CpG25723149 | 24797680 | Putative Promoter | 7 |
Probe 16 | CpG22804000 | 24797691 | Putative Promoter | 7 |
Probe 17 | CpG07504598 | 24797786 | Putative Promoter | 7 |
Probe 18 | CpG15037663 | 24797835 | Putative Promoter | 7 |
Probe 19 | CpG19706795 | 24797839 | Putative Promoter | 7 |
Probe 20 | CpG20764575 | 24797884 | Putative Promoter | 7 |
Probe 21 | CpG06301139 | 24798175 | Upstream Region | 7 |
Probe 22 | CpG26712096 | 24798855 | Upstream Region | 7 |
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Ibrahim, J.; Op de Beeck, K.; Fransen, E.; Peeters, M.; Van Camp, G. The Gasdermin E Gene Has Potential as a Pan-Cancer Biomarker, While Discriminating between Different Tumor Types. Cancers 2019, 11, 1810. https://doi.org/10.3390/cancers11111810
Ibrahim J, Op de Beeck K, Fransen E, Peeters M, Van Camp G. The Gasdermin E Gene Has Potential as a Pan-Cancer Biomarker, While Discriminating between Different Tumor Types. Cancers. 2019; 11(11):1810. https://doi.org/10.3390/cancers11111810
Chicago/Turabian StyleIbrahim, Joe, Ken Op de Beeck, Erik Fransen, Marc Peeters, and Guy Van Camp. 2019. "The Gasdermin E Gene Has Potential as a Pan-Cancer Biomarker, While Discriminating between Different Tumor Types" Cancers 11, no. 11: 1810. https://doi.org/10.3390/cancers11111810