Identification of Prognostic Biomarkers Among FAM83 Family Genes in Human Ovarian Cancer Through Bioinformatic Analysis and Experimental Verification

Figures & data

Table 1 FAM83s Expression in Different Type of Ovarian Cancer and Normal Ovarian Tissues (Oncomine)

Gene	Type of Ovary Cancer vs Ovary	Fold Change	P-value	Dataset
FAM83D	Ovarian Serous Adenocarcinoma vs Peritoneum	6.972	<1.00E-4	Yoshihara Ovarian
	Ovarian Serous Adenocarcinoma vs Ovarian Surface Epithelium	1.705	6.90E-3	Lu Ovarian
	Ovarian Endometrioid Adenocarcinoma vs Ovarian Surface Epithelium	1.680	2.61E-2	Lu Ovarian
FAM83F	Ovarian Serous Adenocarcinoma vs Peritoneum	4.497	3.00E-4	Yoshihara Ovarian
FAM83H	Ovarian Serous Adenocarcinoma vs Ovarian Surface Epithelium	1.644	3.80E-3	Lu Ovarian

Note: Statistic method: Student’s t-test (unpaired, two-tailed).

Abbreviation: vs, versus.

Figure 1 Transcriptional level of FAM83 family members in various types of cancer (ONCOMINE).

Notes: The graph shows the numbers of datasets with statistically significant mRNA overexpression (red) or down-regulated expression (blue) of the target gene. The threshold was designed with following parameters: p-value <0.001, fold change >1.5 and gene rank in the Top 10%. The number on each cell represents the number of datasets that meet the filtering threshold. Cell color is determined by the best gene rank percentile for the analyses within the cell. Student’s t-test was used to identify the difference between two groups.

Figure 2 The mRNA expression levels of FAM83 family members in 426 ovarian cancer tissues and 88 normal ovary tissues (GEPIA) (A–H).

Notes: *Indicates a statistically significant difference between the two groups; Student’s t-test was applied to identify the FAM83 genes expression difference between ovarian cancer and normal ovary tissue.

Figure 3 FAM83 family genes alterations in ovarian cancer (cBioportal).

Notes: (A) Left: OncoPrint visual summary of alterations in FAM83s; right: summary of genetic alteration frequency in FAM83 genes. (B) Analysis of genetic alteration frequency in FAM83 family members in three datasets (TCGA Firehouse Legacy, TCGA Nature 2011 and TCGA PanCancer Atlas). The alterations included amplification, mutations, deep deletions, structural and multiple alterations. Kaplan–Meier analysis for overall survival in patients with or without FAM83 gens alterations, (C) FAM83E; (D) FAM83G and (E) FAM83H.

Figure 4 Prognostic value of FAM83s mRNA levels in patients with OC (OS in Kaplan–Meier plotter).

Notes: (A–G) Prognostic significance of each FAM83 gene in OC. (H) Prognostic HRs of each FAM83 gene in OC. The red and black lines represent high and low expression, respectively. The Log rank test was used to calculate the p-value.

Abbreviations: OC, ovarian cancer; OS, overall survival; HR, hazard ratio.

Figure 5 Prognostic value of FAM83s mRNA levels in patients with OC (PFS in Kaplan–Meier plotter).

Notes: (A–G) Prognostic significance of each FAM83 gene in OC. (H) Prognostic HRs of each FAM83 gene in OC. The red and black lines represent high and low expression, respectively. The Log rank test was used to calculate the p-value.

Abbreviations: OC, ovarian cancer; PFS, progression-free survival; HR, hazard ratio.

Table 2 The Prognostic Value of FAM83D and FAM83H in Different Subtypes

Subtype	FAM83D		FAM83H
	HR (95% CI)	p-value	HR (95% CI)	p-value
Histology
Endometrioid	1.7E9 (0-Ihf)	0.043*	3.23 (0.45–23.12)	0.22
Serous	1.41 (1.09–1.83)	0.0086*	1.33 (1.06–1.66)	0.014*
Stage
1+2	10.76 (1.41–81.88)	0.0041*	2.90 (1.05–8.01)	0.031*
3+4	1.42 (1.13–1.78)	0.0023*	1.27 (0.98–1.66)	0.075
Grade
1	2.51 (0.69–9.21	0.15	2.29 (0.71–7.36)	0.15
2	1.54 (0.99–2.39)	0.053	1.78 (1.08–2.92)	0.022*
3	1.38 (1.06–1.79)	0.015*	1.20 (0.92–1.55)	0.17
TP53
Mutated	0.76 (0.51–1.12)	0.16	1.87 (1.27–2.75)	0.0012*
Wild type	2.24 (0.78–6.39)	0.12	2.28 (0.82–6.37)	0.1

Note: *p<0.05; Each subgroup was analyzed using the Kaplan–Meier method.

Abbreviation: HR, hazard ratio.

Figure 6 Functional enrichment analysis of FAM83D and FAM83H in ovarian cancer.

Notes: (A) Significant pathway enrichment of FAM83D co-expression genes. (B) Significant biological process enrichment of FAM83D co-expressed genes. (C) Significant pathway enrichment of FAM83H co-expression genes. (D) Significant biological process enrichment of FAM83H co-expressed genes; statistic method: Spearman correlation analysis.

Figure 7 Co-expression analysis of FAM83D/H and cell cycle pathway-related genes.

Notes: (A) Cell cycle-related genes significantly associated with FAM83D. (B) Cell cycle-related genes significantly associated with FAM83H. Statistic method: Spearman correlation analysis.

Figure 8 Correlation between FAM83D/H expression and immune infiltration.

Notes: (A and B) Relationship between FAM83D/H expression and six immune cell infiltration including B cell, CD8+ T cell, CD4+ T cell, Macrophage, Neutrophil and Dendritic cell. (C and D) The relationship between somatic copy number alterations of FAM83D/H and immune cell infiltration;

Figure 9 IHC analysis and clinicopathological analysis of FAM83H in OC.

Notes: (A) Immunohistochemical detection of FAM83H in OC tissues. (B) Four typical immunohistochemical sections with score 1, 2, 3 and 4, respectively. (C) Association between the expression of FAM83H and different clinical features in OC; Student’s t-test (unpaired, two-tailed) or the Wilcoxon signed-rank test were used to analyze the relationships between FAM83H expression and different clinicopathological feature; *p<0.05; **p<0.01; ***p<0.001.

Abbreviations: OC, ovarian cancer; ns, not statistically significant.

Table 3 Summary of Bioinformation Analysis of FAM83 Genes in Ovarian Cancer

Gene	Expression		Prognosis (Kaplan–Meier Plotter)
	Oncomine	GEPIA	OC (OS)	OC (PFS)
FAM83A		√		√
FAM83B			√	√
FAM83C
FAM83D	√	√	√	√
FAM83E		√	√	√
FAM83F	√
FAM83G
FAM83H	√	√	√	√

Notes: The expression and prognosis of FAM83D and FAM83H in OC represents statistically significant in three databases (Oncomine, GEPIA and Kaplan–Meier plotter); √ Indicates that the result is statistically significant.

Abbreviations: OS, overall survival; PFS, progression-free survival.