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Table 1 Genomic TNBC subtypes and assignment of TNBC cell lines to subtypes

From: Triple-negative breast cancer molecular subtyping and treatment progress

TNBC subtype Genetic abnormalities Cell line Subtype correlationA (p value) Histology Mutations
Basal-like 1 Cell cycle gene expression
DNA repair gene (ATR-BRCA pathway)
Proliferation genes
HCC2157
HCC1599
HCC1937
HCC1143
HCC3153
MDA-MB-468
HCC38
0.66 (0.00)
0.62 (0.00)
0.28 (0.00)
0.26 (0.00)
0.24 (0.00)
0.19 (0.06)
0.19 (0.01)
DC
DC
DC
IDC
DC
DC
BRCA1; STAT4; UTX
BRCA2; TP53; CTNND1; TOP2B; CAMK1G
BRCA1; TP53; MAPK13; MDC1
TP53
BRCA1
PTEN; RB1; SMAD4; TP53
CDKN2A; TP53
Basal-like 2 Growth factor-signaling pathways (EGFR, MET, NGF, Wnt/β-catenin, IGF-1R)
Glycolysis, gluconeogenesis
Expression of myoepithelial markers
SUM149PT
CAL-851
HCC70
HCC1806
HDQ-P1
0.30 (0.00)
0.25 (0.00)
0.24 (0.04)
0.22 (0.00)
0.18 (0.17)
INF
IGA
DC
ASCC
IDC
BRCA1
RB1; TP53
PTEN; TP53
CDKN2A; TP53; UTX
TP53
Immunomodulatory Immune cell processes (CTLA4, IL2, IL7 pathways, antigen processing/presentation) Gene signature for medullary BC (rare TNBC with a favorable prognosis) HCC1187
DU4475
0.22 (0.00)
0.17 (0.00)
DC
DC
TP53; CTNNA1; DDX18; HUWE1; NFKBIA
APC; BRAF; MAP 2 K4; RB1
Mesenchymal-like Cell motility
Cell differentiation
Growth factor signaling
EMT
BT-549
CAL-51
CAL-120
0.21 (0.00)
0.17 (0.00)
0.09 (0.00)
IDC
AC
AC
PTEN; RB1; TP53
PIK3CA
TP53
Mesenchymal stem-like Similar to M+
Low proliferation
Angiogenesis genes
HS578T
MDA-MB-157
SUM159PT
MDA-MB-436
MDA-MB-231
0.29 (0.00)
0.25 (0.00)
0.14 (0.00)
0.13 (0.00)
0.12 (0.00)
CS
MBC
ANC
IDC
IDC
CDKN2A; HRAS; TP53
NF1; TP53
PIK3CA; TP53 HRAS
BRCA1; TP53
BRAF; CDKN2A; KRAS; NF2; TP53; PDGFRA
Luminal androgen receptor Androgen receptor gene
Luminal gene expression pattern
Molecular apocrine subtype
MDA-MB-453
SUM185PE
HCC2185
CAL-148
MFM-223
0.53 (0.00)
0.39 (0.00)
0.34 (0.00)
0.32(0.00)
0.31 (0.00)
AC
DC
AC
AC
PIK3CA; CDH1; PTEN
PIK3CA
PIK3CA
PIK3CA; RB1; TP53; PTEN
PIK3CA; TP53
  1. Data from Lehmann et al. [14]
  2. Abbreviations: AC adenocarcinoma, ANC anaplastic carcinoma, ASCC acantholytic squamous cell carcinoma, CS carcinosarcoma, DC ductal carcinoma, IDC invasive ductal carcinoma, IGA invasive galactophoric adenocarcinoma, INF inflammatory ductal carcinoma, MC metaplastic carcinoma and MBC medullary breast cancer
  3. AGene expression (GE) data for TNBC cell lines (GSE-10890 and E-TABM-157) were correlated (Spearman) to the centroids of the GE signatures for each TNBC subtype. GE data from both the TNBC tumors and cell lines were combined so that each gene was standardized to have mean = 0 and SD = 1. GE profiles from the cell lines were correlated to the centroids for each of the 6 TNBC subtypes. Cell lines were assigned to the TNBC subtype with the highest correlation, and those that had low correlations (< 0.1) or were similar between multiple subtypes (p > 0.05) were considered unclassified