Comprehensive Analysis and Identification of Prognostic Biomarkers and Therapeutic Targets Among FAM83 Family Members for Gastric Cancer

Abstract

Background: Gastric cancer (GC) is one of the most common and poor prognosis malignancy in the world. The Family with sequence similarity 83 (FAM83) comprises of eight members of A-H. Accumulating evidence confirmed important roles for FAM83 family in tumorigenesis and progression. However, the prognostic values of FAM83 family in GC still have not been clarified. Methods: ONCOMINE, UALCAN, GEPIA, THE HUMAN PROTEIN ATLAS, Kaplan-Meier Plotter, cBioPortal, DAVID, STRING and TIMER databases and R software were adopted in this study. Results: In this study, we demonstrated that the mRNA levels of FAM83 B/C/D/H were significantly up-regulated in stomach adenocarcinoma (STAD), but the protein level of FAM83G/H were remarkable lowly in STAD. Next, FAM83C/D/G/H were significantly associated with tumor stages in STAD patients. Then, the mutation rate of FAM83 family members in STAD patients was 46%, and the highest mutation rate was FAM83H (23%). Furthermore, the functions of FAM83 family and their 259 co-expression genes were primarily related to Shigellosis, RNA degradation and Ribosome biogenesis in eukaryotes pathway. Besides, we have established the prognostic model of FAM83 family in STAD, including the prognostic model of STAD patients (FAM83C/D/G), STAD with lymph node metastasis (FAM83C/D/G/H) and STAD with ERBB2 high expression (FAM83G/H). FAM83C/D high expression with a poor prognosis, while FAM83G/H high expression with a favorable prognosis of STAD. Additionally, we found that the expression of FAM83C/D/G/H were significantly correlated with the infiltration of six types of immune cells [B cells, CD8⁺T cells, CD4⁺T cells, macrophages and Myeloid dendritic cells (DC)], whereas CD4⁺T cells and Macrophage cells have higher risk scores (HR > 1) when FAM83C lowly expression and FAM83D highly expression. The risk score of NK cells was significantly reduced when FAM83G lowly expression and FAM83H highly expression (HR < 1). Conclusion: These findings suggested that FAM83C/D/G/H might play key roles in STAD tumorigenesis and progression, and FAM83C/D might be risk factors but FAM83G/H might be favorable prognostic factors for STAD patients. In addition, CD4⁺T cells and Macrophage cells may be the promoters of FAM83D in progression of STAD, while NK cells may promote the protective effect of FAM83H on STAD patients.

Keywords: FAM83 family members; gastric cancer; immune cell infiltration; lasso regression analysis; nomogram prognostic model; prognostic biomarker.

FIGURE 1

The mRNA expression level of FAM83 family in STAD and other distinct types of cancer (ONCOMINE and GEPIA database). (A) This figure shows the number of datasets with statistically significant mRNA up-regulation (red) or down-regulation (blue) in the FAM83 family. The student’s t-test was used to compare different transcriptions. The cut-off values of p-value and fold change were as follows: p-value: 0.05, fold change: 2, gene rank: 10%, data type: mRNA. (B) Relative level of FAM83 family members in STAD. FAM83H was the highest mRNA expression in STAD.

FIGURE 2

(A) The mRNA expressions of FAM83B/C/H were found to be over-expressed in STAD tissues compared to normal samples in UALCAN. ^∗∗∗p < 0.001 and ^∗p < 0.05. (B) The mRNA expressions of FAM83B/D/H were discovered to be over-expressed in STAD tissues compared to normal stomach tissues in GEPIA2.0. Significance of difference estimated by Student’s t-test and analysis of variance (ANOVA). ^∗p < 0.01.

FIGURE 3

The IHC analysis of FAM83 family with prognostic values. Differentially expressed proteins of FAM83 family members with prognostic values in STAD and normal stomach tissues in The Human Protein Atlas database.

FIGURE 4

(A–H) The correlation between mRNA expression levels of FAM83 family and individual cancer stage in STAD patients (UALCAN). FAM83D/E/F/G/H mRNA expressions were significantly related to patients’ individual cancer stage, while mRNA expressions of FAM83A/B/C were not remarkably associated with patients’ individual cancer stages. Significance of difference estimated by student’s t-test considering unequal variance. ^∗p < 0.05, ^∗∗p < 0.01 and ^∗∗∗p < 0.001.

FIGURE 5

Genetic alterations in FAM83 family members and their correlation with each members in STAD (cBioPortal). (A,B) Genetic alterations in different expressed FAM83 family members in STAD. (C) Lollipop plot displaying mutation distribution and protein domains for FAM83 family members in STAD with the labeled recurrent hotspots. (D) Correlations of different FAM83 family members with each other in STAD.

FIGURE 6

The enrichment analysis of FAM83 family members and their 259 co-expression genes in STAD patients (STRING and DAVID). (A) The PPI network with high confidence (0.7) and hide disconnected nodes in the network. The nodes meant proteins, and the edges meant protein interaction. (B) Displayed the results of GO enrichment analysis with bar graphs. (C–E) BP, CC and MF in GO enrichment analysis. (F) KEGG enrichment analysis.

FIGURE 7

(A–G) Prognostic analysis of FAM83 family members in gastric cancer patients (Kaplan–Meier plotter). The Kaplan-Meier plotter database was used to plot OS, FP, and PPS survival curves at the threshold of p-value < 0.05 to compare patients with high (red) and low (black) expression of FAM83 family members in gastric cancer.

FIGURE 8

(A–P) The prognostic value of FAM83 family members in STAD patients in the overall survival (OS) and disease free survival (DFS) curve (GEPIA2.0).

FIGURE 9

The construction of prognostic model of gene signature from FAM83 family in STAD (TCGA)by LASSO analysis. (A) Coefficients of selected features are shown by lambda parameter. (B) Partial likelihood deviance vs. log (λ) was drawn using LASSO Cox regression model. (C) The relationship between survival status—risk score rank and expression of FAM83 family. (D) Kaplan–Meier survival plots of the two groups (high risk and low risk). (E) ROC curves of the survival model in STAD.

FIGURE 10

Univariate and multivariate Cox regression analyses and establishment and verification of Nomogram for the FAM83 family genes and clinical risk factors of STAD patients. (A,B) Forest plots for hazard ratios (HRs) of survival-associated FAM83 family genes and clinical risk factors in STAD. (C) Nomogram to predict the 1-, 2-, 3-, and 5-year overall survival of STAD patients. (D) Calibration curve for the overall survival nomogram model in the discovery group. A dashed diagonal line represents the ideal nomogram, and the brown line, blue line, orange line and purple line represent the 1-, 2-, 3-, and 5-year observed nomograms, respectively.

FIGURE 11

(A–D) Immune Cell Infiltration of FAM83 FAM83C/D/G/H in STAD (TCGA). The box diagram on the left represented the score distribution of FAM83C/D/G/H in STAD tissues and normal tissues, where the horizontal axis represents different groups of samples, the vertical axis represents the gene expression distribution, where different colors represent different groups, and the upper left corner represents the significance p-value test method. The diagram on the left were immune cell score heat map, where different colors represent the expression trend in different samples, and the significance of two groups of samples passed the Wilcox test. Asterisks represent levels of significance. The asterisk represents the degree of importance (*p < 0.05, **p < 0.01, ***p < 0.001).

FIGURE 12

(A–D) The correlation between different expressed FAM83 family members and immune cell infiltration (TIMER2.0).

FIGURE 13

(A–J) The Kaplan-Meier curves for the immune infiltrates, expression level of FAM83C/D/G/H and STAD. The infiltration level is divided into low and high levels, and the hazard ratio and p-value for Cox model and the log-rank p-value for KM curve were shown on the KM curve plot (TIMER2.0).