PDE1B, a potential biomarker associated with tumor microenvironment and clinical prognostic significance in osteosarcoma

Abstract

PDE1B had been found to be involved in various diseases, including tumors and non-tumors. However, little was known about the definite role of PDE1B in osteosarcoma. Therefore, we mined public data on osteosarcoma to reveal the prognostic values and immunological roles of the PDE1B gene. Three osteosarcoma-related datasets from online websites were utilized for further data analysis. R 4.3.2 software was utilized to conduct difference analysis, prognostic analysis, gene set enrichment analysis (GSEA), nomogram construction, and immunological evaluations, respectively. Experimental verification of the PDE1B gene in osteosarcoma was conducted by qRT-PCR and western blot, based on the manufacturer's instructions. The PDE1B gene was discovered to be lowly expressed in osteosarcoma, and its low expression was associated with poor OS (all P < 0.05). Experimental verifications by qRT-PCR and western blot results remained consistent (all P < 0.05). Univariate and multivariate Cox regression analyses indicated that the PDE1B gene had independent abilities in predicting OS in the TARGET osteosarcoma dataset (both P < 0.05). GSEA revealed that PDE1B was markedly linked to the calcium, cell cycle, chemokine, JAK STAT, and VEGF pathways. Moreover, PDE1B was found to be markedly associated with immunity (all P < 0.05), and the TIDE algorithm further shed light on that patients with high-PDE1B expression would have a better immune response to immunotherapies than those with low-PDE1B expression, suggesting that the PDE1B gene could prevent immune escape from osteosarcoma. The PDE1B gene was found to be a tumor suppressor gene in osteosarcoma, and its high expression was related to a better OS prognosis, suppressing immune escape from osteosarcoma.

Keywords: Biomarker; Immunity; Osteosarcoma; PDE1B; Prognosis.

Figure 1

The expression of PDE1B in osteosarcoma; (A) Venn diagram for gene filtration; (B) PDE1B gene expression in GSE28424 dataset; (C) PDE1B gene expression in GSE33382 dataset; (D) PDE1B gene survival analysis in TARGET osteosarcoma dataset; (E) qRT-PCR results of PDE1B gene in osteosarcoma cell lines; (F) Western blot results of PDE1B gene in osteosarcoma cell lines; (G) Bar chart of western blot results.

Figure 2

Boxplots of PDE1B gene expression distribution in (A) gender of female and male; (B) race of African, Asian, and White; (C) first event of relapse, censored or none; (D) disease at diagnosis of metastatic or nonmetastatic; (E) primary tumor site of arm/hand/pelvis, and leg/foot.

Figure 3

Univariate and multivariate cox regression analyses; (A) Univariate cox regression analyses; (B) Multivariate cox regression analyses.

Figure 4

Nomogram and its evaluations; (A) Nomogram; (B) 1-year calibration plot; (C) 3-year calibration plot; (D) 5-year calibration plot.

Figure 5

PDE1B-related signaling pathways; (A) Calcium pathway; (B) Cell cycle pathway; (C) Chemokine pathway; (D) JAK STAT pathway; (E) VEGF pathway; (F) All of these five pathways.

Figure 6

Correlations between PDE1B expression and (A) immune checkpoints genes; (B) m6A regulator genes; (C) VEGF pathway genes; *P < 0.05; **P < 0.01; ***P < 0.001; ns not significant.

Figure 7

Correlations between PDE1B expression and immunity in osteosarcoma; (A) Proportions of tumor immune cells infiltration levels in tissues of TARGET osteosarcoma dataset; (B) 22 kinds of immune cells in high-PDE1B and low-PDE1B subgroups; (C) Correlation analyses between PDE1B and Macrophages M0 cells infiltration levels; (D) Correlation analyses between PDE1B and T cells gamma delta infiltration levels; (E) Tumor microenvironment evaluations; (F) Correlation analyses between PDE1B and ESTIMATE score; (G) Correlation analyses between PDE1B and immune score; (H) Correlation analyses between PDE1B and stromal score; *P < 0.05; **P < 0.01; ***P < 0.001; ns not significant.

Figure 8

Evaluating osteosarcoma patients’ PDE1B gene expression for immunotherapies by TIDE dataset; (A) TIDE scores in high-PDE1B and low-PDE1B subgroups; (B) T cell dysfunction scores in high-PDE1B and low-PDE1B subgroup; *P < 0.05;***P < 0.001.