In the human genome, approximately 95% of genes undergo AS 2. While AS provides a means for cells to generate diverse protein isoforms, mounting evidence suggests that cancer-related AS alterations play a crucial role in the onset and maintenance of human diseases 32. Research has indicated that AS can serve as effective biomarkers for predicting a range of tumor prognosis and immunotherapy outcomes 33. Associations have been established between tumor-associated AS events, immune infiltration, and patient prognosis 34. Furthermore, abnormal activation of the PCP signaling pathway has been closely linked to cancer development 10 35. Despite both PCP pathway gene anomalies and AS changes being significant features in tumor initiation and progression, relevant investigations are still in their infancy. Therefore, our study comprehensively analyzes the interplay between PCP-related AS genes and tumor microenvironment, and immune characteristics, identifying valuable AS events associated with tumor prognosis. This work provides meaningful guidance for the identification of biomarkers and immunotherapeutic targets.
In this study, the set of genes related to the PCP signaling pathway was sourced from MSigDB, RGD, GeneCards, and Reactome databases. RNA-seq data and clinical information were obtained from the TCGA database. AS event data was extracted from the TCGA SpliceSeq database. We investigated 115 PCP-related AS events from 9,812 pan-cancer patients. Preliminary identification revealed that ES is the most prevalent AS type in tumor genes. Subsequently, using Lasso regression and multivariate Cox regression analyses, we systematically identified 12 PCP-related AS events associated with tumor prognosis (UBA52|48476|AD, NPHP3|66811|AT, PSMB3|40592|ES, AP2S1|50601|ES, PSMA6|27226|ES, PSMA4|32106|ES, PSMA2|79318|AT, PTK7|76246|AT, UBC|25164|RI, NPHP3|66810|AT, PRICKLE3|89099|AT, and PRICKLE4|76139|AA). Based on these 12 AS events, we constructed a risk score model to analyze the survival prognosis of tumor patients. Kaplan-Meier survival analysis and clinical correlation analysis indicated that higher risk scores were associated with poorer patient prognosis. To assess the clinical utility of the risk model, we integrated risk scores and clinical parameters to develop a nomogram prognostic model for quantitatively predicting the survival prognosis of tumor patients. ROC and calibration curves confirmed the favorable predictive performance of this model.
In recent years, an increasing number of studies have revealed the role of AS in modulating changes in the immune microenvironment, thereby influencing the development of cancer immunotherapy strategies 36. Using the ESTIMATE algorithm, CIBERSORT analysis, and ssGSEA, we conducted analyses of tumor microenvironment, immune infiltration, and immune functionality in high- and low-risk groups. The results demonstrated that patients with higher risk scores exhibited characteristics of lower tumor purity and higher immune scores. Furthermore, within the high-risk group, there was a lower content of CD8 + T cells, functionally active NK cells, and Tregs closely associated with the tumor. Moreover, a majority of immune-related functional genes were upregulated in the high-risk group. These findings suggest that tumors may utilize various mechanisms to suppress the activity of immune cells, creating an immune-inhibitory microenvironment, thereby diminishing the immune cell's capacity to attack tumor cells 37. Immune checkpoint molecules, which are components of the co-inhibitory signaling pathways, play a role in maintaining immune tolerance but are frequently exploited by tumor cells to evade immune surveillance 38. In the investigation of the relationship between risk scores and immune checkpoints, we identified that overexpression of four key immune checkpoint genes (CTLA4, LAG3, PDCD1, and VSIR) was associated with adverse tumor prognosis. Overall, our analysis sheds light on the tumor immune microenvironment in high-risk patients, potentially offering new directions for the development of relevant ICIs to mitigate tumor immune evasion and improve patient prognosis.
To explore PCP-associated AS genes with prognostic relevance in cancer, we conducted a correlation analysis between PCP-related AS genes and risk scores. The results indicated that overexpression of PSMA2, PSMB3, PSMA6, AP2S1, PTK7, PSMA4, UBA52, and PRICKLE3 might be associated with unfavorable tumor prognosis. Subsequently, we observed that differentially expressed AS genes (PRICKLE3, PSMA4, and AP2S1) exhibited significantly higher expression in normal tissues compared to tumor tissues. Consequently, we performed survival prognosis and immune feature analyses on PRICKLE3, PSMA4, and AP2S1. PRICKLE3, a protein-coding gene in the PCP signaling pathway, is primarily involved in regulating cell polarity and tissue development 39. Previous research has suggested that PRICKLE3 is significantly upregulated in bladder cancer tissues and may be linked to tumor invasion and prognosis 40. Our findings demonstrated that high PRICKLE3 expression was associated with poorer OS in tumor patients, particularly in males and those with higher age, advanced stage, higher T, and higher N stage. Despite the higher immune score observed in the high PRICKLE3 expression group, its expression was inversely correlated with infiltration levels of memory B cells and functionally active NK cells. The PSMA4 gene encodes a subunit of the proteasome and is involved in regulating intracellular protein degradation processes. Elevated PSMA4 expression has been implicated in the prognosis of lung and breast cancer patients 41 42. Our results indicated that high PSMA4 expression was associated with unfavorable survival status in tumor patients, although immune scores, immune infiltration levels, and functional scores were relatively favorable. AP2S1 encodes the σ1 subunit of the adaptor protein complex 2 and plays a significant role in regulating processes such as endocytosis, transport, and cell polarity. While there have been reports suggesting a potential tumor-suppressive role of AP2S1 43, limited studies have unveiled its role in cancer. We observed that elevated AP2S1 expression was linked to poorer survival outcomes in tumor patients. Interestingly, high AP2S1 expression was associated with better matrix scores, immune infiltration, and functional scores. In conclusion, our results indicate a close association between the expression of PRICKLE3, PSMA4, and AP2S1 and tumor prognosis and immunity. However, the biological functions of these genes in tumors warrant further exploration.
In this study, TIMER2.0 was employed to assess the relationship between PRICKLE3, PSMA4, and AP2S1 and immune characteristics across various tumors, enhancing the effectiveness of our research. Our investigation revealed that PRICKLE3, PSMA4, and AP2S1 were associated with tumor purity in the majority of cancer types. Furthermore, the expression of PRICKLE3, PSMA4, and AP2S1 displayed distinct correlations with different levels of immune cell infiltration within tumor types. For instance, in many tumor types, PSMA4 exhibited a positive correlation with CD8 + T cell infiltration levels, while showing a negative correlation with memory B cells. Moreover, immune checkpoints play a crucial role in mediating tumor immune evasion 44. Through our analysis, we found that except for AP2S1, the expression of PRICKLE3 and PSMA4 showed a positive correlation with immune checkpoint genes (CD274 and CTLA4) in most tumor types. This suggests that PRICKLE3 and PSMA4 might exert similar immune inhibitory effects by promoting the expression of CD274 and CTLA-4, thereby facilitating immune escape. Copy number alterations constitute a major source of genetic changes in human cancers and play a significant role in cancer progression 45 46. Our analysis of CNAs indicated that the high amplification of PRICKLE3, PSMA4, and AP2S1 is likely a crucial factor in promoting tumor growth and proliferation. Specifically, the high amplification of PRICKLE3 was closely associated with PRAD patients, while the high amplification of PSMA4 and AP2S1 was correlated with BRCA patients. In summary, these findings suggest the potential of PRICKLE3, PSMA4, and AP2S1 to serve as biomarkers and drug targets for cancer immunotherapy, providing valuable insights for the development of novel immunotherapeutic drugs.
SF genes, acting as upstream regulators of AS events, indirectly promote tumor initiation and progression by influencing the AS process 47. Thus, uncovering the regulatory network between AS events and SF genes holds significant importance. Within the SF-AS regulatory network, we identified 26 SF genes significantly associated with 10 adverse AS events and 9 favorable AS events. The construction of this network provides deeper insights into the regulatory mechanisms of AS in cancer, offering novel perspectives for identifying therapeutic targets, biomarkers, and immune modulation mechanisms.
Through MR analysis, we discovered that NPHP3 and UBA52, genes identified through multivariable Cox regression within the transcriptome, are strongly associated with the occurrence and progression of pan-cancer at the GWAS genetic level. Both genes serve as protective factors against cancer development. This validates the negative correlation between the expression of NPHP3 in our transcriptome and risk scores. Additionally, UBA52 may indirectly influence cancer risk by affecting eQLT through genetic variations, resulting in a reduction in the risk of cancer occurrence. Through further verification using BWMR, we have found that NPHP3 and UBA52 are indeed associated with the progression of cancer. Therefore, delving deeper into the relationship between AS genes related to the PCP pathway and tumors is warranted.
Nevertheless, our study has inherent limitations. First, the information in the database used in this study may come from different laboratories and studies, so there are problems in terms of quality and consistency. We hope that more standardized methods will be adopted in future studies to ensure data consistency. Second, the mechanisms of AS events and SF genes require fine molecular analysis to reveal their exact role in cancer initiation and development.