Transcriptomic analyses identify key differentially expressed genes and clinical outcomes between triple-negative and non-triple-negative breast cancer

Figures & data

Figure 1 Overview of the study.

Abbreviation: GO, gene ontology.

Table 1 Gene ontology analysis and KEGG pathway analysis of differentially expressed genes

Expression	Category	Term	Gene count	%	P-value
Upregulated	GOTERM_BP_FAT	GO:0010468–regulation of gene expression	67	29.78	4.33E-02
	GOTERM_BP_FAT	GO:0008283–cell proliferation	62	27.56	1.76E-12
	GOTERM_BP_FAT	GO:0007049–cell cycle	60	26.67	1.12E-13
	GOTERM_BP_FAT	GO:0022402–cell cycle process	53	23.56	1.79E-13
	GOTERM_BP_FAT	GO:0009893–positive regulation of metabolic process	52	23.11	1.85E-02
	GOTERM_MF_FAT	GO:0003700–transcription factor activity, sequence-specific DNA binding	30	13.33	9.13E-04
	GOTERM_MF_FAT	GO:001071–nucleic acid binding transcription factor activity	30	13.33	9.13E-04
	GOTERM_MF_FAT	GO:0042802–identical protein binding	28	12.44	4.28E-03
	GOTERM_MF_FAT	GO:0043565–sequence-specific DNA binding	26	11.56	2.74E-03
	GOTERM_MF_FAT	GO:0046983–protein dimerization activity	24	10.67	2.29E-02
	GOTERM_CC_FAT	GO:0005654–nucleoplasm	57	25.33	1.38E-03
	GOTERM_CC_FAT	GO:0005829–cytosol	57	25.33	3.22E-02
	GOTERM_CC_FAT	GO:0005694–chromosome	28	12.44	6.51E-05
	GOTERM_CC_FAT	GO:0044427–chromosomal part	27	12.00	2.06E-05
	GOTERM_CC_FAT	GO:0030054–cell junction	26	11.56	4.76E-02
	KEGG_PATHWAY	hsa04110: cell cycle	12	5.33	3.12E-07
	KEGG_PATHWAY	hsa05206: microRNAs in cancer	9	4.00	2.49E-02
	KEGG_PATHWAY	hsa04310: Wnt signaling pathway	7	3.11	7.24E-03
Downregulated	GOTERM_BP_FAT	GO:0023051–regulation of signaling	92	22.01	2.92E-04
	GOTERM_BP_FAT	GO:0010646–regulation of cell communication	91	21.77	2.67E-04
	GOTERM_BP_FAT	GO:0070887–cellular response to chemical stimulus	79	18.90	1.24E-03
	GOTERM_BP_FAT	GO:0009966–regulation of signal transduction	78	18.66	3.57E-03
	GOTERM_BP_FAT	GO:0010033–response to organic substance	78	18.66	1.50E-02
	GOTERM_MF_FAT	GO:0005102–receptor binding	55	13.16	1.19E-05
	GOTERM_MF_FAT	GO:0042802–identical protein binding	37	8.85	1.88E-02
	GOTERM_MF_FAT	GO:0044877–macromolecular complex binding	37	8.85	3.48E-02
	GOTERM_MF_FAT	GO:0046983–protein dimerization activity	34	8.13	3.11E-02
	GOTERM_MF_FAT	GO:0008289–lipid binding	27	6.46	1.19E-03
	GOTERM_CC_FAT	GO:0005576–extracellular region	141	33.73	1.42E-05
	GOTERM_CC_FAT	GO:0044421–extracellular region part	131	31.34	1.43E-07
	GOTERM_CC_FAT	GO:0031988–membrane-bounded vesicle	126	30.14	4.59E-08
	GOTERM_CC_FAT	GO:0043230–extracellular organelle	98	23.44	4.37E-06
	GOTERM_CC_FAT	GO:1903561–extracellular vesicle	98	23.44	4.30E-06
	KEGG_PATHWAY	hsa04022: cGMP–PKG signaling pathway	10	2.39	1.36E-02
	KEGG_PATHWAY	hsa04152: AMPK signaling pathway	9	2.15	6.66E-03
	KEGG_PATHWAY	hsa04972: pancreatic secretion	8	1.91	5.23E-03

Figure 2 The 16 upregulation identified genes.

Notes: (A) Details of the frequency alteration of the 16 identified upregulated genes in the cBio Cancer Genomics Portal. (B) The frequency of alteration. (C) HORMAD1 and SOX8 status in different subtypes of breast cancer.

Abbreviations: HER2, human epidermal receptor 2; TNBC, triple-negative breast cancer.

Table 2 The 16 upregulation identified genes

Gene symbol	Gene name	Probe set	Log2 FC	P-value	Adj. P-value
PROM1	Prominin 1	204304_s_at	2.87	5.67E-16	1.27E-14
GABRP	Gamma-aminobutyric acid type A receptor pi subunit	205044_at	2.86	1.79E-13	2.71E-12
FABP7	Fatty acid binding protein 7	205030_at	2.82	1.91E-11	2.06E-10
		205029_s_at	2.09	5.40E-11	5.40E-10
ROPN1	Rhophilin associated tail protein 1	231535_x_at	2.71	3.17E-22	1.63E-20
VGLL1	Vestigial like family member 1	215729_s_at	2.64	1.18E-17	3.36E-16
SHC4	SHC adaptor protein 4	235238_at	2.54	2.87E-19	1.01E-17
		230538_at	2.04	8.23E-22	4.00E-20
HORMAD1	HORMA domain containing 1	223861_at	2.51	1.55E-18	4.93E-17
FOXC1	Forkhead box C1	1553613_s_at	2.47	4.22E-23	2.42E-21
EN1	Engrailed homeobox 1	220559_at	2.46	2.10E-29	2.39E-27
PSAT1	Phosphoserine aminotransferase 1	223062_s_at	2.45	8.26E-18	2.41E-16
FERMT1	Fermitin family member 1	60474_at	2.42	3.64E-42	1.45E-39
ART3	ADP-ribosyltransferase 3	210147_at	2.35	7.36E-18	2.17E-16
ELF5	E74 like ETS transcription factor 5	220625_s_at	2.33	2.10E-11	2.25E-10
ROPN1B	Rhophilin associated tail protein 1B	220425_x_at	2.32	4.39E-20	1.73E-18
SOX8	SRY-box 8	226913_s_at	2.15	2.99E-17	8.04E-16
KRT6B	Keratin 6B	213680_at	2.1	8.73E-09	5.92E-08

Abbreviation: FC, fold change.

Figure 3 qRT-PCR validation of HORMAD1 and SOX8 expression in breast cancer.

Notes: HORMAD1 (A) and SOX8 (D) mRNA levels determined by qRT-PCR in a normal mammary cell line and in breast cancer cell lines. β-actin serves as the internal reference. The error bars represent the standard deviations from triplicates of one representative experiment. *P<0.05 and **P<0.01. (B) HORMAD1 mRNA levels in TNBC and the corresponding paired normal adjacent tissues (Normal 1). (C) HORMAD1 mRNA levels in non-TNBC and the corresponding paired normal adjacent tissues (Normal 2). (E) SOX8 mRNA levels in TNBC and the corresponding paired normal adjacent tissues (Normal 1). (F) SOX8 mRNA levels in non-TNBC and the corresponding paired normal adjacent tissues (Normal 2).

Abbreviations: qRT-PCR, quantitative RT-PCR analysis; TNBC, triple-negative breast cancer.

Figure 4 Association of HORMAD1 with RFS and OS in breast cancer (KM Plotter Tool cohort).

Notes: Kaplan–Meier survival curves of (A) RFS for breast cancer, (B) RFS for TNBC, (C) RFS for Luminal A/B, (D) RFS for HER2+ and (E) OS for breast cancer (left), ER-negative breast cancer (middle) and ER-positive breast cancer (right). Red line = high HORMAD1 group, black line = low HORMAD1 group. The cutoff value between high and low is computed by KM Plotter Tool, and the best performing threshold is used as a cutoff. Number at risk table below graph shows the number of cases that reached the endpoint (number of events), the number of cases that did not reach the endpoint (number censored) and the total number of cases.

Abbreviations: HER2, human epidermal receptor 2; OS, overall survival; RFS, relapse-free survival; TNBC, triple-negative breast cancer.

Figure 5 Association of HORMAD1 with prognosis in 240 TNBC patients from SYSUCC (SYSUCC cohort).

Notes: (A) DFS curves for 240 TNBC patients with high or low HORMAD1 levels. (B) OS curves for 240 TNBC patients with high or low HORMAD1 levels. Red line = high HORMAD1 group, black line = low HORMAD1 group.

Abbreviations: DFS, disease-free survival; OS, overall survival; SYSUCC, Sun Yat-sen University Cancer Center; TNBC, triple-negative breast cancer.

Table 3 Association between HORMAD1 and clinicopathological characteristics in triple-negative breast cancer

Variables	HORMAD1		P-value
	Low	High
	No. ()	No. ()
Age (years)			0.273
≤50	108 (74.5)	37 (25.5)
>50	77 (81.1)	18 (18.9)
Menopause			0.272
No	107 (74.3)	37 (25.7)
Yes	78 (81.3)	18 (18.8)
Tumor size			<0.001a
≤2.0 cm	62 (93.9)	4 (6.1)
>2.0 cm	123 (70.7)	51 (29.3)
Lymph node infiltrated			0.002a
No	105 (85.4)	18 (14.6)
Yes	80 (68.4)	37 (31.6)
TNM staging			<0.001a
I–II	157 (83.5)	31 (16.5)
III–IV	28 (53.8)	24 (46.2)
Histological grade			0.321b
G1	3 (100)	0 (0)
G2	112 (79.4)	29 (20.6)
G3	185 (77.1)	55 (22.9)

Notes: Bold figures indicate statistically significant.

a P<0.05.

b Using Fisher’s exact test.