Clinical and Genomic Implications of Luminal and Basal Subtypes Across Carcinomas

Clin Cancer Res. 2019 Apr 15;25(8):2450-2457. doi: 10.1158/1078-0432.CCR-18-3121. Epub 2018 Dec 20.


Purpose: Carcinomas originate from epithelial tissues, which have apical (luminal) and basal orientations. The degree of luminal versus basal differentiation in cancer has been shown to be biologically important in some carcinomas and impacts treatment response.

Experimental design: Although prior studies have focused on individual cancer types, we used a modified clinical-grade classifier (PAM50) to subtype 8,764 tumors across 22 different carcinomas into luminal A, luminal B, and basal-like tumors.

Results: We found that all epithelial tumors demonstrated similar gene expression-based luminal/basal subtypes. As expected, basal-like tumors were associated with increased expression of the basal markers KRT5/6 and KRT14, and luminal-like tumors were associated with increased expression of the luminal markers KRT20. Luminal A tumors consistently had improved outcomes compared with basal across many tumor types, with luminal B tumors falling between the two. Basal tumors had the highest rates of TP53 and RB1 mutations and copy number loss. Luminal breast, cervical, ovarian, and endometrial tumors had increased ESR1 expression, and luminal prostate, breast, cervical, and bladder tumors had increased androgen receptor (AR) expression. Furthermore, luminal B tumors had the highest rates of AR and ESR1 mutations and had increased sensitivity in vitro to bicalutamide and tamoxifen. Luminal B tumors were more sensitive to gemcitabine, and basal tumors were more sensitive to docetaxel.

Conclusions: This first pan-carcinoma luminal/basal subtyping across epithelial tumors reveals global similarities across carcinomas in the transcriptome, genome, clinical outcomes, and drug sensitivity, emphasizing the biological and translational importance of these luminal versus basal subtypes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antineoplastic Agents / pharmacology
  • Antineoplastic Agents / therapeutic use
  • Biomarkers, Tumor
  • Carcinoma / diagnosis*
  • Carcinoma / drug therapy
  • Carcinoma / genetics*
  • Carcinoma, Basal Cell / diagnosis*
  • Carcinoma, Basal Cell / drug therapy
  • Carcinoma, Basal Cell / genetics*
  • Cell Line, Tumor
  • Computational Biology / methods
  • Drug Resistance, Neoplasm / genetics
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic / drug effects
  • Genetic Association Studies* / methods
  • Genetic Predisposition to Disease*
  • Genomics* / methods
  • Humans
  • Kaplan-Meier Estimate
  • Mutation
  • Prognosis
  • Transcriptome


  • Antineoplastic Agents
  • Biomarkers, Tumor