Myc pathway-guided alternative splicing events predict the overall survival of lung squamous cell carcinoma

Figures & data

Figure 1. Identification of Hallmark gene sets-associated AS events. (A, B) The activities of tumor signaling pathways in normal, early-stage and advance-stage of LUSC were calculated by the PEGASAS analysis. Hallmark_Myc_Targets_V1 (A) and Hallmakr_Apical_Surface (B) were shown. (C, D) GO BP analysis of Hallmark_Myc_Targets_V1 (C) and Hallmakr_Apical_Surface (D)-associated AS events. (E) KEGG pathway enrichment of Hallmakr_Apical_Surface (left) and Hallmark_Myc_Targets_V1 (right)-associated AS events.

Figure 2. Screening of prognosis-related AS events and AS-based LUSC subtype classification. (A) Heatmap of PSI value of differential AS events between normal, early-stage and advance-stage LUSC. (B) Unsupervised heatmap of PSI value of prognostic AS events. (C) The Kaplan-Meier survival curve of LUSC clusters. (D–G) distribution of patient tumor stage (D), age (E), gender (F) and pathologic_N (G) in LUSC clusters.

Table 1. Univariate Cox regression analysis of prognosis-related AS events.

AS events	HR (95% CI)	P value
ID_9625	1.638 (1.242–2.161)	0.000
ID_81187	1.503 (1.138–1.984)	0.004
ID_9624	0.670 (0.509–0.883)	0.004
ID_81185	0.668 (0.506–0.882)	0.004
ID_24704	0.672 (0.510–0.886)	0.005
ID_24705	1.478 (1.121–1.948)	0.006
ID_37798	1.469 (1.115–1.936)	0.006
ID_69089	1.465 (1.112–1.930)	0.007
ID_59424	1.460 (1.106–1.927)	0.008
ID_59422	0.698 (0.529–0.921)	0.011
ID_38130	0.710 (0.540–0.934)	0.014
ID_49932	0.710 (0.539–0.935)	0.015
ID_66486	1.408 (1.069–1.856)	0.015
ID_38131	1.400 (1.064–1.841)	0.016
ID_18268	1.397 (1.058–1.845)	0.018
ID_79157	0.732 (0.557–0.963)	0.026
ID_28797	0.739 (0.561–0.973)	0.031
ID_59273	0.739 (0.561–0.973)	0.031
ID_49685	1.350 (1.026–1.776)	0.032
ID_63079	0.697 (0.500–0.972)	0.033
ID_63415	1.349 (1.023–1.777)	0.034
ID_79158	1.340 (1.019–1.762)	0.036
ID_62294	0.745 (0.565–0.983)	0.037
ID_66487	0.747 (0.567–0.984)	0.038
ID_13995	0.751 (0.570–0.988)	0.041
ID_29320	1.330 (1.011–1.751)	0.042
ID_68258	0.752 (0.572–0.990)	0.042
ID_13994	1.323 (1.005–1.741)	0.046
ID_68257	1.322 (1.005–1.740)	0.046

HR: hazard ratio; CI: confidence interval.

Figure 3. Construction and evaluation of the predictive efficacy of the prognostic model. (A) λ selection in LASSO model. (B–K) The Kaplan-Meier survival curve of OS-related AS events.

Table 2. Optimized prognostic AS events.

AS ID	Gene symbol	AS type	LASSO coefficient	HR
ID 28797	EFCAB11	AT	−0.122	0.739
ID 29320	PPP2R5C	AT	0.506	1.33
ID 38130	VPS9D1	AP	−0.785	0.71
ID 59273	EPB41L1	ES	−0.542	0.739
ID 63415	PPARG	AP	0.096	1.349
ID 66486	CCDC14	AP	0.916	1.408
ID 79157	AQP1	AP	−0.392	0.732
ID 81185	DNAJC2	AT	−2.373	0.668
ID 81187	DNAJC2	AT	0.004	1.503
ID 9625	C4BPB	AT	0.129	1.638

Figure 4. Evaluation of the predictive efficacy of the prognostic model. (A–C) PS scores distribution (Up), patient survival information (Middle), and heatmap for PSI of 10 prognostic AS events (Low) in the training set (A), validation set (B), and whole set (C). (D–F) The Kaplan-Meier survival curve of high- and low-risk groups in the training set (D), validation set (E), and whole set (F). (G) distribution of LUSC clusters in high- and low-risk groups.

Figure 5. Regulatory network of AS and splicing factors. The diamond nodes represent splicing factors (SF); the ellipse nodes represent favorable alternative splicing (AS) events, and the circle nodes represent unfavorable AS events; the lines represent the correlation between AS events and SFs, respectively.

Figure 6. GSEA pathway enrichment analysis. The top 5 differential KEGG pathways enriched in the high-risk group (A) and low-risk group (B).

Data availability statement

The (log2(fpkm+1) RNAseq data and phenotype data of Lung Squamous Cell Carcinoma (LUSC) used in this study is available publicly from The Cancer Genome Atlas (TCGA) database at https://xenabrowser.net/. The percent spliced index (PSI) values of alternative splicing events of TCGA-LUSC samples were available from the SpliceSeq database http://projects.insilico.us.com/TCGASpliceSeq/. GSE19188 and GSE30219 datasets were available from the Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc.