Integrated Analysis of CD1A Immune Infiltration and Competing Endogenous RNA Networks in COAD

Figures & data

Figure 1 Expression of CD1A in COAD and Across Various Cancer Types. (A) Differential expression of CD1A in multiple tumor types as indicated by the GENT2 database. (B) Evaluation of CD1A expression levels across different tumor types using the TIMER database. (C) Comparative analysis of CD1A expression in COAD versus normal tissues in the TCGA database. (D) Analysis of CD1A expression in COAD compared to paired normal tissues using the TCGA database. (E) Examination of CD1A expression differences between COAD and normal tissues using the GSE21510 dataset. (F) Assessment of CD1A expression in COAD versus normal tissues using the GSE22598 dataset. (G) Investigation of CD1A expression in COAD relative to normal tissues with the GSE37364 dataset. (H) Analysis of CD1A expression in COAD cell lines (SW480 and HCT116) and normal human colon epithelial cell line (HCoEpiC).

Notes: *P < 0.05; **P < 0.01; ***P < 0.001.

Abbreviations: COAD, Colon adenocarcinoma.

Table 1 Correlation Analysis of CD1A mRNA Expression with Clinicopathological Features in the TCGA COAD Cohort

Characteristics	Low expression of CD1A	High expression of CD1A	P value
n	239	239
Age, n (%)			0.576
> 65	145 (30.3%)	139 (29.1%)
<= 65	94 (19.7%)	100 (20.9%)
Gender, n (%)			0.044
Female	102 (21.3%)	124 (25.9%)
Male	137 (28.7%)	115 (24.1%)
Pathologic T stage, n (%)			0.025
T1	5 (1%)	6 (1.3%)
T2	30 (6.3%)	53 (11.1%)
T3	168 (35.2%)	155 (32.5%)
T4	36 (7.5%)	24 (5%)
Pathologic N stage, n (%)			0.004
N0	141 (29.5%)	143 (29.9%)
N1	43 (9%)	65 (13.6%)
N2	55 (11.5%)	31 (6.5%)
Pathologic M stage, n (%)			0.039
M0	158 (38.1%)	191 (46%)
M1	39 (9.4%)	27 (6.5%)
Pathologic stage, n (%)			0.007
Stage I	28 (6%)	53 (11.3%)
Stage II	103 (22.1%)	84 (18%)
Stage III	63 (13.5%)	70 (15%)
Stage IV	39 (8.4%)	27 (5.8%)
Histological type, n (%)			0.426
Adenocarcinoma	205 (43.3%)	198 (41.9%)
Mucinous adenocarcinoma	32 (6.8%)	38 (8%)

Figure 2 Analysis of CD1A’s biological functions in COAD. (A) Identification of genes significantly associated with CD1A in COAD. (B) Heatmap illustrating the top 50 genes positively correlated with CD1A in COAD. (C) Heatmap depicting the top 50 genes negatively correlated with CD1A in COAD. (D) GO functional annotation analysis for genes co-expressed with CD1A. (E) KEGG pathway enrichment analysis for genes co-expressed with CD1A. (F) Protein-protein interaction network involving CD1A.

Figure 3 Correlation between CD1A Expression and Immune Cell Infiltration in COAD. (A) Significant correlation of CD1A expression with the infiltration levels of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells in COAD. (B) Impact of CD1A CNV on the infiltration levels of CD8+ T cells, B cells, and dendritic cells in COAD. (C) Comparative analysis of immune cell subtype proportions in groups with high versus low CD1A expression.

Notes: *P < 0.05; **P < 0.01; ***P < 0.001.

Table 2 Analysis of the Correlation Between CD1A and Immunological Markers of Immune Cells

Gene markers	Gene markers	Rho	P value
B cell	CD19	0.168	<0.001
	CD20	−0.048	0.685
	CD70	0.163	0.001
CD8+T Cell	CD8A	0.189	<0.001
	CD8B	0.133	0.008
	CD25	0.338	0.003
Tfh	CD183	0.226	0.055
	CD185	−0.025	0.835
	CD278	0.229	0.01
Th1	CD212	0.225	0.056
	CD191	0.189	0.109
	CD195	0.275	0.019
Th2	CD194	0.35	0.002
	CD198	0.343	0.003
	CD365	0.025	0.834
Th17	CD360	−0.187	0.112
	IL23R	0.139	0.005
	CD196	0.254	0.03
Treg	FOXP3	0.46	<0.001
	CD73	0.073	0.537
	CD127	−0.111	0.35
T cell exhaustion	PD-1	−0.117	0.325
	CTLA4	0.331	<0.001
	LAG3	0.157	0.002
Macrophage	CD68	0.228	<0.001
	CD11b	0.255	0.029
M1 Macrophage	NOS2	0.062	0.209
	IRF5	0.17	<0.001
M2 Macrophage	CD163	0.232	<0.001
	CD206	0.342	0.003
TAM	CCL2	0.307	<0.001
	CD86	0.329	<0.001
Monocyte	CD14	0.317	<0.001
	CD33	0.322	<0.001
Natural killer cell	CD57	−0.097	0.417
	KIR3DL1	−0.016	0.747
	CD7	0.209	<0.001
Neutrophil	CD16	0.106	0.37
	CD55	0.042	0.397
Dendritic cell	CD1C	0.698	<0.001
	CD141	0.291	0.013

Figure 4 Correlation between CD1A expression and m6A-related genes in COAD. (A-F) Correlation analysis between CD1A expression and FTO, HNRNPA2B1, IGF2BP2, METTL3, RBM15 and RBMX. (G) Differences in the expression of m6A-related genes between CD1A high-expression and low-expression groups in COAD.

Note: *P < 0.05.

Abbreviations: m6A, N6-methyladenosine.

Figure 5 Correlation analysis of CD1A with target miRNAs. (A) Correlation analysis of CD1A expression with hsa-miR-33b-5p expression. (B) Correlation analysis of CD1A expression with that of hsa-miR-516b-5p. (C) Correlation analysis of CD1A expression with that of hsa-miR-589-3p.

Figure 6 CeRNA network construction of CD1A in COAD. (A) Prediction of target lncRNA of has-miR-33b-5p using starbase and miRNet. (B) Prediction of target lncRNA of has-miR-33b-5p using starbase and miRNet. (C-F) Correlation analysis of miRNAs with targeted lncRNAs. (G) Sankey diagram showing the lncRNA-miRNA-mRNA regulatory network of CD1A.