Bioinformatics analysis for the identification of Sprouty-related EVH1 domain-containing protein 3 expression and its clinical significance in thyroid carcinoma

Abstract

The poorly differentiated thyroid carcinoma (THCA) subtype is associated with an aggressive disease course, a less favorable overall prognosis, and an increased risk of distant organ metastasis. In this study, our objective was to explore the potential utility of the Sprouty-related EVH1 domain-containing protein 3 (SPRED3) as a biomarker for early diagnosis and prognosis in THCA patients. The differentially expressed prognostic-related genes associated with THCA were identified by querying The Cancer Genome Atlas (TCGA) database. The difference in the expression of the SPRED3 gene between thyroid carcinoma (THCA) tissues and normal tissues was analyzed using data from The Cancer Genome Atlas (TCGA) and further validated through immunohistochemistry. Univariate and multivariate Cox regression models were used, along with clinical information from THCA patients, to analyze the prognostic value of the SPRED3 gene in THCA patients. Functional enrichment analysis was subsequently performed to elucidate the molecular mechanisms underlying the regulatory effects of the SPRED3 gene on thyroid carcinoma. Additionally, we calculated the percentage of infiltrating immune cells in THCA patients and evaluated their correlation with SPRED3 gene expression. Compared with those in noncancerous thyroid tissue, the gene and protein expression levels of SPRED3 were found to be elevated in thyroid carcinoma tissues. Furthermore, the expression of SPRED3 in thyroid carcinoma exhibited significant correlations with tumor location, histological grade, pathological stage, and tumor node metastasis classification (TNM) stage. Univariate and multivariate Cox proportional hazards (Cox) regression analyses demonstrated that SPRED3 could serve as an independent prognostic factor for predicting the overall survival of THCA patients. The results of functional enrichment analysis suggested the potential involvement of SPRED3 in the regulation of extracellular matrix organization, epidermal development, signaling receptor activator activity, skin development, receptor ligand activity, glycosaminoglycan binding, neuroactive ligand‒receptor interaction, the IL-17 signaling pathway, and the PI3K-Akt signaling pathway. Additionally, there were significant correlations between the expression level of the SPRED3 gene and the infiltration of various immune cells (eosinophils, central memory T cells, neutrophils, macrophages, and NK cells) within the thyroid tumor microenvironment. SPRED3 can be used as a prognostic biomarker in patients with THCA could potentially be therapeutic target for THCA.

Figure 1

The identification of differentially expressed mRNA associated with prognosis in thyroid carcinoma, showcasing (A) a volcanic map depicting the differential expression pattern of mRNA, and (B) a Venn diagram highlighting the overlap between differentially expressed mRNA and genes related to prognosis.

Figure 2

The expression level of SPRED3 is evaluated and exhibits exceptional diagnostic predictive value for patients with THCA. (A) Comparative analysis of SPRED3 mRNA expression levels in tumor and adjacent normal tissues across multiple malignancies. (B) The SPRED3 mRNA levels were quantified using RNA-seq data obtained from tumor samples and their matched normal tissues in the TCGA database. (C) Analysis of sequencing data revealing differential expression of SPRED3 mRNA between normal and THCA (thyroid carcinoma) tissues. (D) Validation of SPRED3 mRNA expression through RNA sequencing in paired samples of THCA and normal thyroid tissues, utilizing publicly available GTEx platform data. (E) ROC curve illustrating the diagnostic value assessment of SPRED3 expression in THCA samples.

Figure 3

Box plot evaluating SPRED3 mRNA expression differences among THCA patients with different clinical characteristics including disease stages (pathologic N stage) (A), tumor pathologic stages (B), histologic types (C), residual tumor (D), neoplasm location (E), and the state of extra-thyroidal extension (F).

Figure 4

High SPRED3 expression predicts a significantly lower overall survival rate in THCA patients. (A) Kaplan–Meier curve illustrating the comparison of overall survival between subgroups of THCA patients with high/low SPRED3 mRNA expression; (B–F) comparison of overall survival among different subgroups of THCA patients based on age, gender, pathologic stages, histologic types, and extra thyroidal extension.

Figure 5

Nomogram curve was constructed to predict the probability of overall survival (OS) in patients at 1-, 3-, and 5-year intervals. The predictive factors included clinical stage, pathologic stage, and SPRED3 expression (A). Additionally, the nomogram was used to predict the 1-year OS in THCA population, as well as the 3-year and 5-year OS (B).

Figure 6

The differentially expressed genes were ranked based on the correlation factor, and subsequently, the gene list was subjected to GO/KEGG analysis for clustering purposes (A), and the correlation between infiltrated immune cells and SPRED3 expression levels in clinical samples of THCA patients was investigated.

Figure 7

The protein expression level of SPRED3 was assessed in both the adjacent tissues (A) and the THCA tumor sample (B).

Figure 8

The flowchart depicting the assessment of SPRED3 expression and its clinical significance in thyroid carcinoma.