Lung Adenocarcinoma and Squamous Cell Carcinoma Gene Expression Subtypes Demonstrate Significant Differences in Tumor Immune Landscape

Abstract

Introduction: Molecular subtyping of lung adenocarcinoma (AD) and lung squamous cell carcinoma (SCC) reveal biologically diverse tumors that vary in their genomic and clinical attributes.

Methods: Published immune cell signatures and several lung AD and SCC gene expression data sets, including The Cancer Genome Atlas, were used to examine immune response in relation to AD and SCC expression subtypes. Expression of immune cell populations and other immune related genes, including CD274 molecule gene (CD274) (programmed death ligand 1), was investigated in the tumor microenvironment relative to the expression subtypes of the AD (terminal respiratory unit, proximal proliferative, and proximal inflammatory) and SCC (primitive, classical, secretory, and basal) subtypes.

Results: Lung AD and SCC expression subtypes demonstrated significant differences in tumor immune landscape. The proximal proliferative subtype of AD demonstrated low immune cell expression among ADs whereas the secretory subtype showed elevated immune cell expression among SCCs. Tumor expression subtype was a better predictor of immune cell expression than CD274 (programmed death ligand 1) in SCC tumors but was a comparable predictor in AD tumors. Nonsilent mutation burden was not correlated with immune cell expression across subtypes; however, major histocompatibility complex class II gene expression was highly correlated with immune cell expression. Increased immune and major histocompatibility complex II gene expression was associated with improved survival in the terminal respiratory unit and proximal inflammatory subtypes of AD and in the primitive subtype of SCC.

Conclusions: Molecular expression subtypes of lung AD and SCC demonstrate key and reproducible differences in immune host response. Evaluation of tumor expression subtypes as potential biomarkers for immunotherapy should be investigated.

Keywords: Adenocarcinoma; Gene expression; Immune response; Lung cancer; PD-L1; Squamous cell carcinoma.

Figure 1.

Heatmaps of Bindea et al. showing immune cell signature expression, other immune signatures, and individual immune markers in lung adenocarcinoma and squamous cell carcinoma gene expression data sets.^, TRU, terminal respiratory unit; PP, proximal proliferative; PI, proximal inflammatory; Tcm, central memory Tcell; Tem, effector memory T cell; Thl, type 1 T helper cell; Th2, type 2 T helper cell; TFH, T follicular helper cell; Th17, T-helper 17 cell; Treg, regulatory T cell; Tγδ, γδ T cell; NK, natural killer; DC, dendritic cell; iDC, immature dendritic cell; aDC, activated dendritic cell; pDC, plasmacytoid dendritic cell; IFN, interferon; PD-L1, programmed death ligand 1; PD-L2, programmed death ligand 2; PDCD1, programmed cell death 1; CTLA4, cytotoxic T-lymphocyte associated protein 4; MHC II, major histocompatibility complex class II.

Figure 2.

Association strength (adjusted r²) between CD274 molecule gene (CD274) (programmed death ligand 1 [PD-L1]) expression and immune signature versus strength between subtype and immune signature for 13 adaptive immune cell (AIC) expression signatures in adenocarcinoma (AD) and squamous cell carcinoma (SCC) data sets. Association between subtype and AIC was greater for some AICs in AD and for all AICs tested in SCC. Tcm, central memory T cell; Tem, effector memory Tcell; Th1, type 1 T helper cell; Th2, type 2 T helper cell; TFH, T follicular helper cell; Th17, T helper 17 cell; Treg, regulatory T cell; Tγδ, γδ T cell.

Figure 3.

Reproducibility of T-cell signature gene expression subtype patterns across multiple adenocarcinoma data sets^,,, and squamous cell carcinoma data sets.^,,, RNA sequencing (RNA-Seq Kit [Illumina, San Diego, CA]) and microarrays from both Affymetrix (Santa Clara, CA) and Agilent (Santa Clara, CA). TCGa, The Cancer Genome Atlas; TRU, terminal respiratory unit; PP, proximal proliferative; PI, proximal inflammatory.

Figure 4.

Adenocarcinoma (AD) and squamous cell carcinoma (SCC) subtype nonsilent mutation burden (A and B), serine/ threonine kinase 11 gene (STK11) inactivation (mutation and/or deletion) in AD (C), nuclear factor erythroid 2, like 2 gene (NFE2L2) expression in SCC (D), and major histocompatibility complex class II (MHC II) signature (Eand F) with association test p values. Mb, megabase; TRU, terminal respiratory unit; PP, proximal proliferative; PI, proximal inflammatory.

Figure 5.

Subtype-specific immune marker hazard ratios and 95% confidence intervals (CIs) for 5-year overall survival in stage I to III adenocarcinoma (A) and stage I to III squamous cell carcinoma (B). Hazard ratios (HRs) correspond to a unit increase in the normalized immune marker and were adjusted for pathological stage using Cox models. Only markers that were significant (nominal p value <0.05) for at least one subtype are shown. Th1, type 1 T helper cells; Th2, type 2 T helper cells; TFH, T follicular helper cell; Th17, T helper 17 cell; Treg, regulatory Tcell; DC, dendritic cell; iDC, immature dendritic cell; PD-L1, programmed death ligand 1; CTLA4, cytotoxic T-lymphocyte associated protein 4; MHC II, major histocompatibility complex class II; TRU, terminal respiratory unit; PP, proximal proliferative; PI, proximal inflammatory.