| Literature DB >> 35756689 |
Debo Yun1,2,3, Xuya Wang1,2, Wenbo Wang1,2, Xiao Ren1,2, Jiabo Li1,2, Xisen Wang1,2, Jianshen Liang1,2, Jie Liu1,2, Jikang Fan1,2, Xiude Ren1,2, Hao Zhang1,2, Guanjie Shang1,2, Jingzhang Sun1,2, Lei Chen1,2, Tao Li1,2, Chen Zhang2, Shengping Yu1,2, Xuejun Yang1,2,4.
Abstract
Background: Ferroptosis is a form of programmed cell death (PCD) that has been implicated in cancer progression, although the specific mechanism is not known. Here, we used the latest DepMap release CRISPR data to identify the essential ferroptosis-related genes (FRGs) in glioma and their role in patient outcomes.Entities:
Keywords: LASSO analysis; cancer essential genes; clinical outcomes; drug screening; ferroptosis; glioma; risk model
Year: 2022 PMID: 35756689 PMCID: PMC9232254 DOI: 10.3389/fonc.2022.897702
Source DB: PubMed Journal: Front Oncol ISSN: 2234-943X Impact factor: 5.738
The clinical features of TCGA cohort and CGGA cohort.
| TCGA cohort | CGGA cohort | |
|---|---|---|
| Characteristic | N = 551 | N = 619 |
| Age | ||
| Median | 47.21 | 43.44 |
| Gender | ||
| Male | 313 | 356 |
| Female | 238 | 263 |
| Grade | ||
| Grage 2 | 209 | 173 |
| Grage 3 | 232 | 231 |
| Grage 4 | 110 | 215 |
| IDH-status | ||
| IDH_WT | 188 | 258 |
| IDH_Mut | 363 | 316 |
| 1p/19q co-deletion | ||
| Non-codel | 403 | 427 |
| Codel | 148 | 128 |
| Vital status | ||
| Alive | 365 | 296 |
| Dead | 186 | 323 |
Figure 1Flow chart showing the design of the study.
Figure 2Venn diagram showing overlap of 10 genes between the CSEGs and FRGs (A). Top prognosis-associated candidate genes identified by Cox regression (B). Re-filtering of genes in (B) by LASSO (C, D). *p < 0.05, **p < 0.01, ***p < 0.001.
Figure 3Kaplan-Meier curves showing risk scores of FRG signature genes in both training and validation cohorts (p < 0.001) (A, B). tROC curves for one-, three- and five-year survival (C, D). Heatmaps of risk score rankings, survival, and levels of cancer-essential FRGs in the training and validation cohorts (E, F).
Figure 4Relationships between the levels of the seven cancer-essential FRGs and clinical features. Age (A), sex (B), normal versus tumor tissue (C), WHO grade (D), 1p/19q co-deletion status (E), and IDH status (F). Immunohistochemistry showing the protein expression of risk model genes in normal and tumor specimens of The Human Protein Atlas (G). ns, p≥0.05, *p < 0.05, **p < 0.01, ***p < 0.001.
Figure 5Survival analysis by the risk model in relation to subgroups of clinical features in the training (A) and validation cohorts (B).
Figure 6Comprehensive analyses of genomic alterations, immune cell infiltration, and immune checkpoint expression between the different risk groups. Distribution of sex, age, IDH status, 1p/19q condel status, and the top 20 most frequently mutated genes are illustrated for each cohort (A, B). Heatmap showing the CIBERSORT scores of different immune cell distributions in the different subgroups (C). Dot plot showing immune cell CIBERSORT scores and the expression levels of immune checkpoint gene in the high- and low-risk groups (D, E). ns, no significance,*p < 0.05, **p < 0.01, ***p < 0.001.
Figure 7Univariate and multivariate analyses of clinical features in relation to prognosis (A, B). Nomograms for prediction of OS and PFI (C, D). Nomogram calibration using OS and PFI for predicted and actual one- three-, and five-year outcomes (E, F). DCA of nomograms for OS and PFI for one- three-, and five-year survival (G, H).
Figure 8Enrichment analysis of cancer-essential FRG signature genes in the TCGA cohort. The top 30 gene sets of HALLMARK (A), KEGG (B), and Reactome (C).
Figure 9Drug connectivity analysis using alteration-specific transcriptional (CLUE and iLINCS). Pan-cancer in CLUE (A), pan-cancer in iLINCS (B), and glioma in iLINCS (C) identifying 20 compounds that enhance or reverse the signature (highlighted with documented mechanisms). Compounds showing negative correlations with AUC values and FRG scores for glioma cells were identified from GDSC1 and GDSC2. (D, E).