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 |