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. 2024 Sep 13;103(37):e39511.
doi: 10.1097/MD.0000000000039511.

PANoptosis-related molecular clustering and prognostic signature associated with the immune landscape and therapy response in breast cancer

Affiliations

PANoptosis-related molecular clustering and prognostic signature associated with the immune landscape and therapy response in breast cancer

Yiming Cao et al. Medicine (Baltimore). .

Abstract

Breast cancer (BC) remains one of the most pervasive and complex malignancies. PANoptosis represents a recently identified cellular mechanism leading to programmed cell death. However, the prognostic implications and influence on the immune microenvironment of BC pertaining to PANoptosis-related genes (PRGs) remain significantly understudied. We conducted differential expression analysis to identify prognostic-Related PRGs by the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Next, we identified the PANoptosis-related molecular subtype using the consensus clustering analysis, and constructed and validated the PANoptosis-related prognostic signature using LASSO and Cox regression analyses. ROC curves were employed to assess the performance of the signatures. Furthermore, drug sensitivity between low- and high-risk group were analysis. Finally, we conducted RT-qPCR to assess the gene expression levels involved in this signature. We categorized BC patients into 2 distinct molecular clusters based on PRGs and identified differentially expressed genes associated with prognosis. Subsequently, BC patients were then divided into 2 gene clusters. The identified PRGs molecular clusters and gene clusters demonstrated association with patient survival, immune system functions, and biological processes and pathways of BC. A prognostic signature comprising 5 genes was established, and BC patients were classified into low- and high-risk groups based on the risk scores. The ROC curves demonstrated that those in the low-risk category exhibited notably extended survival compared to the high-risk group. A nomogram model for patient survival was constructed based on the risk score in conjunction with other clinical features. High-risk group had higher tumor burden mutation, CSC index and lower StomalScore, ImmuneScore, and ESTIMATEScore. Subsequently, we established a correlation between the risk score and drug sensitivity among BC patients. Finally, qRT-PCR results showed that the expression of CXCL1, PIGR, and TNFRSF14 significantly decreased, while CXCL13 and NKAIN were significantly increased in BC tissues. We have developed a molecular clustering and prognostic signature based on PANoptosis to improve the prediction of BC prognosis. This discovery has the potential to not only assist in assessing overall patient prognosis but also to deepen our understanding of the underlying mechanisms of PANoptosis in BC pathogenesis.

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Conflict of interest statement

The authors have no conflicts of interest to disclose.

Figures

Figure 1.
Figure 1.
The flowchart of this study.
Figure 2.
Figure 2.
Expression and genetic alteration of PRGs in breast cancer: (A) Mutation situations of 29 PRGs. (B) Locations of CNV alterations for PRGs on 23 chromosomes. (C) Copy number alterations of PRGs. (D) Expression difference of PRGs. *P < .05; **P < .01; ***P < .001. CNV = copy number variation, PRGs = PANoptosis-related genes.
Figure 3.
Figure 3.
Prognosis significance of PRGs of BC patients in TCGA and GEO in BC: (A–L) The survival curve of CASP1, CASP7, CASP8, FADD, GSDMD, IRF1, NLRC4, RYCARD, RIRK3, TAB2, TNFAIP3, and ZBP1 displays the OS of BC patients. (M) Prognostic network of PRGs. BC = breast cancer, OS = overall survival, PRGs = PANoptosis-related genes.
Figure 4.
Figure 4.
PRG molecular subtypes and their clinicopathological features: (A–C) Identification of 2 molecular subtypes (k = 2) and their correlation area through consensus clustering analysis. (D) PCA showed good distinction between 2 PRGclusters. (E) KM curve indicated that PRGcluster A had longer survival time than PRGcluster B (P = .003). (F) Heatmaps showed the relationship between PRGclusters and clinical features and PRGs expression in breast cancer patients. PRGs = PANoptosis-related genes.
Figure 5.
Figure 5.
Identification of geneclusters based on differentially expressed genes (DEGs): (A and B) GSVA showed the enriched KEGG pathways in PRGclusters. (C) ssGSEA investigated the differences of immune cell infiltration between 2 geneclusters. (D) The Venn diagram shows the intersection of the differentially expressed PRGs. (E and F) GO and KEGG analyses showed the relevant biological processes (BP), cellular components (CC), molecular functions (MF) and pathways. GO = gene ontology, GSVA = gene set variation analysis, KEGG = Kyoto Encyclopedia of Genes and Genomes, PRGs = PANoptosis-related genes.
Figure 6.
Figure 6.
PRG gene subtypes and their clinicopathological features and prognostic risk model: (A–C): Identification of 2 gene subtypes (k = 2) and their correlation area through consensus clustering analysis. (D) KM curve indicated that genecluster A had longer survival time than genecluster B (P = .005). (E) Heatmap showed the association between genecluster and clinical features. (F) Expression levels of PRGs in 2 geneclusters. (G and H) The LASSO regression analysis and partial likelihood deviance on the prognostic genes. (I) Sankey plot showed the correlation between molecular classifications, risk groups and survival status in breast cancer patients. (J and K) Association between risk score and molecular and gene classifications. (L) Expression levels of PRGs in 2 risk groups. *P < .05; **P < .01; ***P < .001. PRGs = PANoptosis-related genes.
Figure 7.
Figure 7.
Validation of the prognostic value of the signatures: (A–C) The KM curve of all sets, training set, and testing set, respectively. (D–F) ROCs for 1-, 3-, and 5-year OS prediction of all sets, training set, and testing set, respectively. (G–O) The risk curve consists of genes expression heat map, risk score curves, and survival status point plot of all sets, training set, and testing set, respectively. (P) The nomogram of the risk score and clinical parameters (age, gender, and stage) of all sets. (Q) The calibration curves displayed the accuracy of the nomogram in the 1st, 3rd, and 5th years. OS = overall survival.
Figure 8.
Figure 8.
To assess the tumor microenvironment, immune checkpoint genes, and tumor mutation burden (TMB) in different groups: (A) Correlation between the abundance of immune cells and 7 genes in the prognostic signature. (B) Differential analyses of TME score among StromalScore, ImmuneScore, and ESTIMATEScore. (C) The somatic gene mutations in high-risk group. (D) The somatic gene mutations in low-risk group. (E) Differential analysis of TMB in high- and low-risk score groups. (F) Positively correlation analysis of PRG Risk score and TMB (R = 0.088, P = .0061). (G) Positively correlation analysis between PRG Risk score and CSC index (R = 0.17, P = 3.8e-08e). *P < .05, **P < .01, ***P < .001. ns = not statistically different, PRGs = PANoptosis-related genes.
Figure 9.
Figure 9.
Verify the mRNA expression levels of the 5 signature genes in the tissues: (A–D) HE staining images in BC tissue and adjacent tissues. (E–I) Differential expression of CXCL1, PIGR, CXCL13, TNFRSF14, and NKAIN in adjacent non-tumor tissues and BC tissues. *P < .05, **P < .01, ***P < .001. BC = breast cancer, ns = not statistically different.

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