Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Oct 4;103(40):e39798.
doi: 10.1097/MD.0000000000039798.

Construction and validation of an immune-related gene signature predictive of survival and response to immunotherapy for colorectal cancer

Affiliations

Construction and validation of an immune-related gene signature predictive of survival and response to immunotherapy for colorectal cancer

Chen Li et al. Medicine (Baltimore). .

Abstract

Colorectal cancer is a common malignant tumor with the second incidence rate and the third mortality rate worldwide. In this study, we identified and validated an immune-related gene signature, explored the clinical and molecular characteristics of the signature-defined risk groups, and assessed its ability in predicting prognosis, immune cell infiltration and immunotherapy responses. The Cancer Genome Atlas database was used as the training set while GSE39582 database as the validation set. Immune-related hub genes were selected by the Least Absolute Shrinkage and Selection Operator-penalized Cox regression model, and the signature was then constructed by the selected genes and their relevant coefficients. Prognostic performance of the signature and the signature-base nomogram models were assessed by time-dependent receiver operating characteristic curves and calibration plots in both training and validation cohorts. Clinical and mutation-related data were downloaded and analyzed to explore their associations with signature-defined risk groups. Proportions of infiltrated immune cells was estimated via CIBERSORT algorithm and immunotherapy response was evaluated by immunophenoscore and tumor immune dysfunction and exclusion scores. Seven among 790 immune-related differentially-expressed genes were selected and use to construct the signature. The signature and signature-base nomograms showed promising prognostic performance in both training and validation cohorts. Signature-defined high-risk group was associated with advanced disease, poor pathological prognostic factors and less active immune infiltration microenvironment. Besides, the response to immunotherapy of high-risk group was predicted to be poorer by immunophenoscore and tumor immune dysfunction and exclusion scores. Our signature proved its efficacy in predicting prognosis, tumor immune microenvironment and responses to immunotherapy in colorectal cancer.

PubMed Disclaimer

Conflict of interest statement

The authors have no conflicts of interest to disclose.

Figures

Figure 1.
Figure 1.
(A) Volcano plot showing differentially expressed genes between CRC samples and normal tissues based on data from TCGA. (B) Venn diagram showing the intersection of CRC DEGs with IRGs. Chord plot visualizing top 5 most enriched GO terms (C) and KEGG pathways (D) and their interactions with DEIRGs. DEIRGs were ordered according to their expression levels (log2FC). CRC = colorectal cancer, DEG = differentially expressed gene, DEIRGs = differentially expressed immune-related genes, GO = Gene Ontology, IRG = immune-related gene, KEGG = Kyoto Encyclopedia of Genes and Genomes, TCGA = The Cancer Genome Atlas.
Figure 2.
Figure 2.
Establishment of IRGPS. (A) Lasso coefficient profile of 93 genes confirmed to have an effect on OS by univariate Cox regression. (B) Mean cross-validated error curve with one-standard-deviation band of Lasso regression model, the left vertical line corresponds to the lambda value with minimum partial likelihood deviance. (C) Forest plot visualizing results of multivariate Cox regression analysis of 7 selected IRDEGs. (D) Heat map of 7 selected IRDEGs and clinicopathological characteristics by risk group in TCGA cohort. (E) Heat map of 7 selected IRDEGs and clinicopathological characteristics by risk group in GSE39582 cohort. IRGPS = immune-related gene prognostic signature, OS = overall survival, TCGA = The Cancer Genome Atlas.
Figure 3.
Figure 3.
Representative immunohistochemical staining images of CDKN2A in CRC tumor tissue (A) and normal tissue (B), LEP in CRC tumor tissue (C) and normal tissue (D), PLCG2 in CRC tumor tissue (E) and normal tissue (F), PTH1R in CRC tumor tissue (G) and normal tissue (H), and SLAMF1 in CRC tumor tissue (I) and normal tissue (J) from The Human Protein Altas. CRC = colorectal cancer, SLAMF1 = signaling lymphocytic activation molecule family member 1.
Figure 4.
Figure 4.
IRGPS predicts OS and PFS in both cohorts. (A) KM curves showing OS of different IRGPS subgroups of TCGA cohort and GSE39582 cohort. (B) KM curves showing PFS of different IRGPS subgroups of TCGA cohort and GSE39582 cohort. (C) Time-dependent ROC curves for the performance of IRGPS in predicting OS in TCGA cohort and GSE39582 cohort. (D) Time-dependent ROC curves for the performance of IRGPS in predicting PFS in TCGA cohort and GSE39582 cohort. IRGPS = immune-related gene prognostic signature, KM = Kaplan–Meier, OS = overall survival, PFS = progression-free survival, ROC = receiver operating characteristic, TCGA = The Cancer Genome Atlas.
Figure 5.
Figure 5.
Construction and validation of IRGPS-based nomograms. (A) Nomogram prediction model for OS of TCGA cohort. (B) Nomogram prediction model for OS of GSE39582 cohort. (C Nomogram prediction model for PFS of TCGA cohort. (D) Nomogram prediction model for PFS of GSE39582 cohort. (E) Time-dependent ROC curves for the performance of nomogram models in predicting OS in TCGA and GSE39582 cohorts. (F) Time-dependent ROC curves for the performance of nomogram models in predicting PFS in TCGA and GSE39582 cohorts. OS = overall survival, PFS = progression-free survival, ROC = receiver operating characteristic, TCGA = The Cancer Genome Atlas.
Figure 6.
Figure 6.
The relationship between IRPGS risk score and clinicopathological features of TCGA cohort (A) and GSE39582 cohort (B). Statistical differences between subgroups were assessed using independent t tests (ns, not significant; *, P < .05; **, P < .01; ***, P < .001; ****, P < .0001). The upper, middle and bottom line of the boxes inside the violins represented the 25th quantile, median and 75th quantile values of risk score. IRGPS = immune-related gene prognostic signature, TCGA = The Cancer Genome Atlas.
Figure 7.
Figure 7.
Mutation profile of IRGPS subgroups and 7 hub genes in TCGA cohort. (A) Oncoplot showing top 10 most frequently-mutated genes of IRGPS high-risk group. (B) Oncoplot showing top 10 most frequently-mutated genes of IRGPS low-risk group. (C) Comparison of TMB between IRGPS subgroups. (D) KM curves showing OS of TMB-high and TMB-low subgroups. (E) Oncoplot showing the mutation frequency of the 7 hub genes of IRGPS. (F) Oncoplot showing the frequency of mutation and copy-number variations of the 7 hub genes from cBioportal database. (G) Summary chart displaying the variant classification, variant type, SNV classes, variants per sample, etc of IRPGI high-risk group. (H) Summary chart of IRGPS low-risk group. IRGPS = immune-related gene prognostic signature, SNV = single nucleotide variation, TCGA = The Cancer Genome Atlas, TMB = total mutation burden.
Figure 8.
Figure 8.
Relative compositions of 22 types of immune cells in different IRGPS subgroups in TCGA (A) and GSE39582 (B) cohorts. The green and blue boxes represent the high-risk group of the 2 cohorts, and the red and yellow boxes represent the low-risk groups. The statistical difference between different subgroups were represented by ns (not significant), *(P < .05), **(P < .01), ***(P < .001), and ****(P < .0001), respectively. IRGPS = immune-related gene prognostic signature, TCGA = The Cancer Genome Atlas.
Figure 9.
Figure 9.
TIDE and IPS analysis of IRGPS subgroups of TCGA cohort. (A) The relationship between IRGPS subgroups and IPS, IPS-PD1/PDL1/PDL2 blocker, IPS-CTLA4 blocker and IPS-CTLA4 & PD1/PDL1/PDL2 blocker. The red and green violins represented high-risk and low-risk groups, respectively. (B) The relationship between IRGPS subgroups and TIDE, dysfunction, exclusion, MSI, CAF, MDSC, TAM.M2 and IFNG enrichment scores. The blue and yellow violins represented high-risk and low-risk groups, respectively. (C) Correlation between IRGPS subgroups and CTL.flag. Patients whose CTL.flag were true (green) had positive gene expression values for 5 cytotoxic T lymphocyte markers (CD8A, CD8B, GZMA, GZMB, and PRF1). Once the expression of one of the markers was negative, CTL.flag was FALSE (red). (D) Comparison of the distribution of predicted responder in high-risk and low-risk groups. TRUE responders (green) were those predicted to respond to immunotherapy by TIDE platform. FALSE responders (red) were those predicted not. CAF = cancer-associated fibroblast. IPS = immunophenoscore, MDSC = myeloid-derived suppressor cell, TIDE = tumor immune dysfunction and exclusion.
Figure 10.
Figure 10.
Expression of major immune checkpoints in IRGPS high-risk and low-risk groups in TCGA (A) and GSE39582 (B) cohorts. The green and blue boxes represent the low-risk group of the 2 cohorts, and the red and yellow boxes represent the high-risk groups. IRGPS = immune-related gene prognostic signature, TCGA = The Cancer Genome Atlas.
Figure 11.
Figure 11.
Graphical flowchart of the study design.

Similar articles

References

    1. Sung H, Ferlay J, Siegel RL, et al. . Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 Cancers in 185 Countries. CA Cancer J Clin. 2021;71:209–49. - PubMed
    1. Arnold M, Sierra MS, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global patterns and trends in colorectal cancer incidence and mortality. Gut. 2017;66:683–91. - PubMed
    1. Siegel RL, Miller KD, Jemal A. Cancer statistics, 2020. CA Cancer J Clin. 2020;70:7–30. - PubMed
    1. Hodi FS, O’Day SJ, McDermott DF, et al. . Improved survival with ipilimumab in patients with metastatic melanoma. N Engl J Med. 2010;363:711–23. - PMC - PubMed
    1. Larkin J, Chiarion-Sileni V, Gonzalez R, et al. . Combined nivolumab and ipilimumab or monotherapy in untreated melanoma. N Engl J Med. 2015;373:23–34. - PMC - PubMed

Publication types

Substances