mRNA and protein levels of FAM3s in patients with THCA
This study was performed to elucidate the latent molecular mechanisms of FAM3 in patients with THCA. Analyses of mRNA and protein levels were performed by using the UALCAN database and the Human Protein Atlas, respectively. mRNA expression levels of four FAM3 members in PTC and normal thyroid tissues were measured by the UALCAN database, as shown in Fig. 1. mRNA expression levels of FAM3A were downregulated in PTC tissues, compared with normal tissues (p = 0.043, Fig. 1A). Furthermore, mRNA expression levels of FAM3B were significantly downregulated in gland papillary carcinoma tissues (p < 0.001, Fig. 1B). Significant upregulation of FAM3C and D mRNA expression levels was observed in thyroid gland papillary carcinoma tissues, compared with normal samples (p < 0.001, Fig. 1C, D).
Protein levels of FAM3s in THCA tissues were analysed using the Human Protein Atlas. Figure 2 shows that FAM3A and FAM3B exhibited intermediate protein expression levels in both normal thyroid tissues and THCA tissues (Fig. 2A–D). FAM3C exhibited intermediate protein expression levels in normal thyroid tissues, but high expression levels in THCA tissues (Fig. 2E, F). Furthermore, FAM3D exhibited low protein expression levels in normal thyroid tissues, but no expression in THCA tissues (Fig. 2G, H).
Overall, our results showed that FAM3C was overexpressed at both mRNA and protein levels in THCA tissues. Considering the significant difference in mRNA expression level of FAM3B between THCA tissues and normal thyroid tissues, we validated the FAM3B protein expression data reported in the Human Protein Atlas. For this validation, we repeated the immunohistochemical analysis of FAM3B, which revealed that the FAM3B protein level was enhanced in THCA tissues (Fig. 3). On the basis of the two results of immunohistochemistry of FAM3B, no definite conclusions could be drawn regarding the use of FAM3B as a biomarker in the pathogenesis of THCA.
Relationships of FAM3 mRNA expression levels with clinicopathological parameters in patients with THCA
Next, the relationships of FAM3 mRNA levels with clinicopathological parameters of patients with THCA were analysed using UALCAN, including an analysis of individual patients’ cancer stages. Figure 4 shows that the mRNA expression levels of FAM3B, C, and D were significantly associated with various stages of cancer (Fig. 4B–D). In particular, patients with more advanced stages of cancer tended to have lower mRNA levels of FAM3B; the lowest mRNA level of FAM3B was observed in patients with stage 2 THCA. Furthermore, the mRNA expression level of FAM3B significantly down-regulated in stages 2 compared with stages 1 of THCA; similar results were observed regarding stages 2 and 3 (Fig. 4B). Patients with more advanced stages of cancer tended to have higher mRNA levels of FAM3C; the highest mRNA level of FAM3C was observed in patients with stage 3 THCA (Fig. 4C). In summary, these results suggested that mRNA expression levels of FAM3B, C, and D were closely associated with clinicopathological parameters in patients with THCA.
Prognostic values of FAM3 mRNA expression levels in patients with THCA
Kaplan–Meier plotter software was used to analyse prognostic values of FAM3 mRNA expression levels in patients with THCA. As shown in Fig. 5, mRNA expression levels of FAM3B, C, and D were significantly associated with prognosis in patients with THCA. First, the association between the combined mRNA level of all four FAM3s and the prognosis of patients with THCA was analysed (Fig. 5A). Notably, the combined mRNA level of all four FAM3s was not associated with overall survival (OS) in patients with THCA (HR = 2, 95% CI: 0.720–5.51, and p = 0.170). Subsequently, associations between the mRNA levels of distinct FAM3s and the prognosis of patients with THCA were analysed. As shown in Fig. 5E and G, higher mRNA expression levels of FAM3B (HR = 0.110, 95% CI: 0.020–0.480, and p < 0.001) and FAM3C (HR = 0.260, 95% CI: 0.1–0.7, and p = 0.004) were significantly associated with favourable OS in patients with THCA, while a higher mRNA expression level of FAM3D was associated with shorter OS in patients with THCA (HR = 2.92, 95% CI: 1.08–7.90, and p = 0.027) (Fig. 5I). Furthermore, the combined mRNA expression level of FAM3A, B, C, and D was associated with disease-free survival (DFS) in patients with THCA (HR = 0.380, 95% CI: 0.170–0.860, and p = 0.016) (Fig. 5B). Additionally, associations between mRNA expression levels of distinct FAM3s and DFS in patients with THCA were analysed. Figure 5 shows that a higher mRNA expression level of FAM3B was associated with shorter DFS in patients with THCA (HR = 0.460, 95% CI: 0.210–0.990, and p = 0.043, HR = 2.49, 95% CI: 1.15–5.39, and p = 0.016) (Fig. 5D, F). These results revealed that mRNA expression levels of FAM3C were significantly associated with prognosis in patients with THCA and might be useful as biomarkers to predict survival of these patients.
Mutations in FAM3s and their relationships with OS and DFS in patients with THCA
Genetic alterations in FAM3s and their relationships with OS and DFS in patients with THCA were performed by Kaplan–Meier plots. Figure 6A shows that FAM3s had low mutation rates in patients with THCA. Among 497 sequenced patients with THCA, only 78 exhibited genetic alterations; thus, the mutation rate was 16%. The mutation rates of FAM3A, B, C, and D were 6%, 4%, 5%, and 1.8%, respectively; the FAM3D gene exhibited the lowest mutation rate. Furthermore, results of Kaplan–Meier and log-rank analyses showed that genetic mutations in FAM3s were not significantly associated with OS and DFS in patients with THCA (Fig. 6B, C).
Functional Enrichment Analysis Of Fam3c In Patients With Thca
The functions of differentially expressed FAM3C were analysed by means of GeneCards and UniProt. Table 1 shows the most highly enriched GO items and KEGG pathways. GO enrichment analysis predicts the functions of target genes from three main perspectives: CCs, BPs, and MFs. Among the highly enriched functions in the BP class, platelet degranulation, signal transduction, multicellular organism development, and negative regulation of gluconeogenesis were associated with the occurrence and development of THCA. In the CC class, the extracellular region, Golgi apparatus, platelet dense granule lumen, cytoplasmic vesicle, and extracellular exosome were enriched, in association with the occurrence and development of THCA. In the MF class, cytokine activity and protein binding were enriched in association with the occurrence and development of THCA. Additionally, four pathways associated with the functions of FAM3C in THCA were observed by KEGG analysis. Among these KEGG pathways, the response to elevated platelet cytosolic Ca2+ was significantly associated with THCA tumorigenesis and progression (Table 1).
Table 1
The enrichment analysis of different expressed FAM3C in THCA (GeneCards and Unprot), including GO enrichment in cellular component terms, biological process terms, and molecular function terms and KEGG enriched terms.
Term ID | Function | Details |
R-HSA-109582.2 | pathway | Platelet activation, signaling and aggregation |
R-HSA-76005.2 | pathway | Response to elevated platelet cytosolic Ca2+ |
R-HSA-114608.3 | pathway | Platelet degranulation |
R-HSA-109582.2 | pathway | Hemostasis |
GO:0002576 | BP | platelet degranulation |
GO:0007165 | BP | signal transduction |
GO:0007275 | BP | multicellular organism development |
GO:0008150 | BP | biological_process |
GO:0045721 | BP | negative regulation of gluconeogenesis |
GO:0005576 | CC | extracellular region |
GO:0005794 | CC | Golgi apparatus |
GO:0031089 | CC | platelet dense granule lumen |
GO:0031410 | CC | cytoplasmic vesicle |
GO:0070062 | CC | extracellular exosome |
GO:0005125 | MF | cytokine activity |
GO:0005515 | MF | protein binding |
Infiltration of FAM3s in immune cells of patients with THCA
FAM3s have been shown to participate in the infiltration of immune cells and inflammatory responses, thereby affecting the prognosis of patients with THCA. Thus, we comprehensively explored correlations between differentially expressed FAM3s and immune cell infiltration using the TIMER database. There were negative correlations between the mRNA expression level of FAM3A and infiltration by B cells (Cor = − 0.309, p < 0.001), CD8 + T cells (Cor = − 0.145, p < 0.001), CD4 + T cells (Cor = − 0.313, p < 0.001), macrophages (Cor = − 0.358, p < 0.001), neutrophils (Cor = − 0.513, p < 0.001), and dendritic cells (Cor = − 0.514, p < 0.001; Fig. 7A). However, the mRNA expression level of FAM3B was positively correlated with the infiltration of B cells (Cor = 0.178, p < 0.001), CD4 + T cells (Cor = 0.205, p < 0.001), macrophages (Cor = 0.230, p < 0.001), neutrophils (Cor = 0.268, p < 0.001), and dendritic cells (Cor = 0.299, p < 0.001; Fig. 7B). A negative correlation was observed between the mRNA expression level of FAM3C and the infiltration of CD8 + T cells (Cor = − 0.378, p < 0.001), whereas positive correlations were observed with the infiltration of B cells (Cor = 0.409, p < 0.001), CD4 + T cells (Cor = 0.392, p < 0.001), macrophages (Cor = 0.356, p < 0.001), neutrophils (Cor = 0.281, p < 0.001), and dendritic cells (Cor = 0.214, p < 0.001; Fig. 7C). Moreover, the mRNA expression level of FAM3D was positively correlated with the infiltration of CD8 + T cells (Cor = 0.101, p = 0.026), whereas it was negatively correlated with the infiltration of B cells (Cor = − 0.228, p < 0.001), CD4 + T cells (Cor = − 0.257, p < 0.001), macrophages (Cor = − 0.213, p < 0.001), neutrophils (Cor = − 0.242, p < 0.001), and dendritic cells (Cor = − 0.214, p < 0.001; Fig. 7D). Correlations were also assessed between differentially expressed FAM3s and infiltration of immune cells. Cox proportional hazard models were used to adjust for the following confounding factors: B cells, CD8 + T cells, CD4 + T cells, macrophages, neutrophils, dendritic, FAM3A, FAM3B, FAM3C, FAM3D, and cancer stage. CD8 + T cells (p = 0.017), dendritic cells (p = 0.047), age (p = 0.000), and stage 4 cancer (p = 0.039) were associated with prognosis in patients with THCA (Table 2).
Table 2
The cox proportional hazard model of FAM3s and six tumor-infiltrating immune cells in THCA (TIMER).
| coef | HR | 95%CI_l | 95%CI_u | p.value | sig |
Age | 0.214 | 1.238 | 1.122 | 1.37 | 0 | *** |
Stage2 | 0.050 | 1.051 | 0.075 | 14.6 | 0.971 | |
Stage3 | 1.506 | 4.51 | 0.387 | 52.6 | 0.229 | |
Stage4 | 3.183 | 24.127 | 1.17 | 498 | 0.039 | * |
Gender male | -0.254 | 0.776 | 0.146 | 4.12 | 0.766 | |
Race Black | 15.649 | 6.25*106 | 0 | Inf | 0.998 | |
Race White | 15.081 | 3.54*106 | 0 | Inf | 0.998 | |
Purity | 6.836 | 931.2 | 11.541 | 7.51*104 | 0.002 | ** |
B_cell | 1.901 | 6.695 | 0 | 2.42*106 | 0.771 | |
CD8_Tcell | -24.859 | 0 | 0 | 0.012 | 0.017 | * |
CD4_Tcell | 7.247 | 1403.8 | 0.009 | 2.18*108 | 0.235 | |
Macrophage | -29.770 | 0 | 0 | 5.25 | 0.063 | |
Neutrophil | -47.797 | 0 | 0 | 7.03*109 | 0.184 | |
Dendritic | 16.608 | 1.63*107 | 1.22 | 2.18*1014 | 0.047 | * |
FAM3A | 1.968 | 7.159 | 0.607 | 84.5 | 0.118 | |
FAM3B | -0.202 | 0.817 | 0.429 | 1.56 | 0.539 | |
FAM3C | 0.711 | 2.035 | 0.522 | 7.93 | 0.306 | |
FAM3D | -0.612 | 0.542 | 0.112 | 2.62 | 0.447 | |
*P < 0.05, |
**P < 0.01, |
***P < 0.001 |