A clinically relevant gene signature in triple negative and basal-like breast cancer

Breast Cancer Research

Table 2 Principal biological phenotypes identified as metagenes among TNBC

Biological component	Metagene name	Correlation within metagene cluster	# of probesets in metagene cluster	Key markers	Reference
Basal-like phenotype	Basal-like	0.61	37	KRT-5,-6, -14, -17, SOX10, SFRP1, ELF5, EPHB3, GABRP	[4]
Apocrine/androgen receptor signalling	Apocrine	0.67	27	AR, FOXA1	[18, 19]
Immune system:					[4, 20, 21, 23–25]
• B-Cell	B-Cell	0.87	48	IgG
• T-Cell	T-Cell	0.84	27	TCR, LCK, ITK
• MHC class II	MHC-2	0.83	14	HLA-DR, -DM, -DP, -DQ
• MHC class I	MHC-1	0.84	17	HLA-A, -B, -C, -E, -F, -G
• Interferone response	IFN	0.76	14	OAS1, OAS2, OAS3, MX1
Stroma*	Stroma	0.83	47	Decorin, Osteonectin, Fibronectin, COL5A1	[26, 27]
Claudin-CD24 signature	Claudin-CD24	0.70	19	CLDN3, CLDN4, CD24, ELF3	[28, 29]
Proliferation	Proliferation	0.74	47	BUB1, CDC2, STK6, BIRC5, TOP2A,	[35]
Blood *	Hemoglobin *	0.63	17	HBA1, HBA2, HBB	[30]
Adipocytes	Adipocyte	0.74	8	FABP4, PLIN, ADIPOQ, ADH1B	[4]
Angiogenesis	VEGF	0.57	7	VEGF, adrenomedullin, ANGPTL4	[34]
Inflammation	IL-8	0.52	4	IL-8, CXCL1, CXCL2	[31, 32]
HOXA gene cluster	HOXA	0.52	8	HOXA-4, -5, -7, -9, -10, -11	[64]
Histone gene cluster	Histone	0.69	19	Histones H2A, H2B	[65]

* The Stroma and Hemoglobin metagenes displayed a bias between datasets related to different biopsy techniques (see Methods).

ISSN: 1465-542X