Biological network-driven gene selection identifies a stromal immune module as a key determinant of triple-negative breast carcinoma prognosis

Figures & data

Figure 1. Methodology flow chart.

Figure 2. Heatmaps of the selected genes in the TNBC training set (upper left) and the TNBC validation sets (upper right: validation, lower left: Ignatiadis, lower right: METABRIC).

Table 1 A. Survival analysis (disease-specific survival). Chemotherapy-treated population. Univariate and multivariate analysis.

		Univariate analysis		Multivariate analysis
139 triple-negative breast cancer patients		DS-survival HR [95% CI]	p value	DS-survival HR [95% CI]	p value
Menopausal status	Pre	1
	Post	1.56 [0.95–2.55]	0.08
Tumor size (mm)	<20 mm	1
	>20 mm	1.03 [0.58–1.82]	0.92
Tumor grade	II	1
	III	1.23 [0.45–3.39]	0.69
Lymph node status	0	1
	1	0.84 [0.42–1.65]	0.61
NPI score	<5.4	1		1
	>5.4	2.15 [1.28–3.60]	0.003	2.30 [1.36–3.89]	0.002
Cellularity	Low	1
	Moderate	0.57 [0.22–1.46]	0.24
	High	0.59 [0.25–1.39]	0.23
P53 status	Wild-type	1
	Mutant	2.42 [1.15–5.09]	0.02
Immunity1 metagene expression	High	1
	Low	0.97 [0.60–1.58]	0.91
Immunity2 metagene expression	High	1		1
	Low	2.59 [1.54–4.34]	0.0002	2.68 [1.59–4.52]	0.0002
Proliferation/DNA damage metagene expression	High	1
	Low	1.13 [0.69–1.84]	0.63
AR-like metagene expression	High	1
	Moderate	1.07 [0.59–1.94]	0.82
	Low	0.98 [0.50–1.94]	0.96
Matrix/Invasion1 metagene expression	High	1
	Low	1.23 [0.76–2.01]	0.40
Matrix2 metagene expression	High	1
	Low	0.99 [0.61–1.61]	0.96

Abbreviations: NPI, Nottingham Prognostic Index; AR, androgen receptor; HR, hazard ratio; CI, confidence interval.

Table 1 B. Survival analysis (disease-specific survival). Chemotherapy-treated population. Two univariate models. Combination of NPI score and Immunity2 metagene expression

139 triple-negative breast cancer patients		DS-survival HR [95% CI]	p value
NPI score/Immunity2 metagene expression	NPI1-2/HighI2	1
	NPI1-2/LowI2	2.90 [1.51–5.56]	0.001
	NPI3	3.98 [2.00–7.92]	8.72 ^10-5
NPI score/Immunity2 metagene expression	NPI1-2/HighI2	1
	NPI1-2/LowI2	2.91 [1.51–5.59]	0.001
	NPI3/HighI2	2.31 [0.96–5.57]	0.06
	NPI3/LowI2	6.30 [2.89–13.78]	3.87^10-6

Abbreviations: NPI, Nottingham Prognostic Index; I2, Immunity2; HR, hazard ratio; CI, confidence interval.

NPI = [0.2 × S] + N + G.

S: tumor size (cm).

N: number of lymph nodes involved (0 = 1, 1−3 = 2, >3 = 3).

G: tumor grade according to Elston and Ellis (Grade I=1, Grade II = 2, Grade III = 3).

Figure 4. String Software connections between our Immunity1 and Immunity2 genes and the genes of eight previously published prognostic immune signatures. Stronger associations between genes are represented by thicker lines. Associations between genes with a coefficient < 0.9 are shown in green. Associations between genes with a coefficient ≥0.9 are shown in red. Associations between genes with a coefficient between 0.4 to 0.7 are not shown.

Table 2 A. Survival analysis (disease-specific survival). Chemotherapy-naive population. Univariate and multivariate analysis.

		Univariate analysis		Multivariate analysis
115 triple-negative breast cancer patients		DS-survival HR [95% CI]	p value	DS-survival HR [95% CI]	p value
Menopausal status	Pre	1
	Post	1.31 [0.56-3.06]	0.53
Tumor size (mm)	<20 mm	1
	>20 mm	2.36 [1.01-5.48]	0.04
Tumor grade	I-II	1
	III	1.33 [0.51-3.49]	0.56
Lymph node status	0	1
	1	3.66 [1.65-8.11]	0.001
NPI score	<3.4	1		1
	3.4-5.4	1.36 [0.47-3.96]	0.57	1.55 [0.53-4.51]	0.43
	>5.4	10.69 [2.74-41.76]	0.001	12.03 [3.05-47.50]	0.0004
Cellularity	Low	1
	Moderate	1.91 [0.54-6.71]	0.31
	High	1.42 [0.41-4.90]	0.58
P53 status	Wild-type	1
	Mutant	0.90 [0.17-4.63]	0.90
Immunity1 metagene expression	High	1
	Low	1.56 [0.76-3.19]	0.22
Immunity2 metagene expression	High	1		1
	Low	2.33 [1.09-4.95]	0.03	2.42 [1.13-5.16]	0.02
Proliferation/DNA damage metagene expression	High	1
	Low	1.14 [0.56-2.32]	0.72
AR-like metagene expression	High	1
	Moderate	0.96 [0.42-2.20]	0.92
	Low	0.74 [0.28-2.00]	0.56
Matrix/Invasion1 metagene expression	High	1
	Low	0.48 [0.23-1.01]	0.06
Matrix2 metagene expression	High	1
	Low	1.31 [0.64-2.66]	0.46

Abbreviations: NPI, Nottingham Prognostic Index; AR, androgen receptor; HR, hazard ratio; CI, confidence interval.

Table 2 B. Survival analysis (disease-specific survival). Chemotherapy-naive population. Univariate analysis. Combination of NPI score and Immunity2 metagene expression.

115 triple-negative breast cancer patients		DS-survival hazard Ratio [95% CI]	p value
NPI score/Immunity2 metagene expression	NPI1-2/HighI2	1
	NPI1-2/LowI2	2.13 [0.95-4.78]	0.07
	NPI3	12.89 [4.07-40.82]	1.37^10−5

Abbreviations: NPI, Nottingham Prognostic Index; I2, Immunity2; HR, hazard ratio; CI, confidence interval.

Figure 3. (A) Kaplan–Meier plots. Disease-specific survival of the chemotherapy-treated population (n = 139). NPI score. Immunity2 metagene. NPI score/Immunity2 metagene. (B) Kaplan–Meier plots. Disease-specific survival of the noCT population (n = 115). NPI score. Immunity2 metagene. NPI score/Immunity2 metagene.

Figure 5. (A) Boxplots of gene expression for the Immunity1 and Immunity2 metagenes, in each breast cancer cell line subtype from the CCLE. (B) Boxplots of gene expression for the Immunity1 and Immunity2 metagenes in each breast cancer cell line subtype from the CGP.