Comparative Analysis of Transcriptomic and Proteomic Expression between Two Non-Small Cell Lung Cancer Subtypes

Abstract

Non-small cell lung cancer (NSCLC) is frequently diagnosed late and has poor survival. The two predominant subtypes of NSCLC, adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), are currently differentially diagnosed using immunohistochemical markers; however, they are increasingly recognized as very different cancer types suggestive of potential for new, more targeted therapies. There are extensive efforts to find more precise and noninvasive differential diagnostic tools. Here, we examined these two NSCLC subtypes for differences that may inform treatment and identify potential novel therapeutic pathways. We presented a comparative analysis of transcriptomic and proteomic expression in tumors from a cohort of 22 NSCLC patients: 8 LUSC and 14 LUAD. Comparing NSCLC subtypes, we found differential gene expression related to cell differentiation for LUSC and cellular structure and immune response regulation for LUAD. Differential protein expression between NSCLC subtypes was related to extracellular structure for LUSC and metabolic processes, including glucose metabolism for LUAD. This direct comparison was more informative about subtype-specific pathways than between each subtype and control (nontumor) tissues. Many of our observations between NSCLC subtypes support and inform existing observations and reveal differences that may aid research seeking to identify and validate novel subtype biomarkers or druggable targets.

Keywords: gene expression; non-small cell lung cancer; proteomics.

Figure 1

Biplots of the LUSC and LUAD subtype comparison. (A) PCA of the normalized gene count matrix numbered with donor identifier. LUSC (blue) and LUAD (red). (B) PCA of the normalized gene count matrix with the genes contributing to the PC directions annotated. (C) PCA of the normalized top 3 peptide intensities numbered with donor identifier. LUSC (light blue) and LUAD (purple). (D) PCA of the normalized top 3 peptide intensities with the protein contributing to the PC directions annotated.

Figure 2

Volcano plots of DEGs and DEPs. Gene names are used on both plots. (A) Comparison of LUSC and LUAD genes (n = 19,859). Thresholds are represented by dotted lines at an FDR of 1% and log₂ fold change of 1.5. NS is any DEG below these thresholds. (B) Comparison of LUSC and LUAD proteins (n = 3872). Thresholds are represented by dotted lines at a p-value of 1% and a log₂ fold change of 1. NS is any DEP below these thresholds.

Figure 3

Bar plots of functional enrichment between NSCLC subtypes. Statistical significance level indicated by the −log₁₀p-value on the x-axis. (A) GO biological processes enriched in NSCLC subtypes. (B) Reactome pathways enriched in NSCLC subtypes. Outputs were not filtered, but for reference, a value of −log₁₀P of 1.3 is equivalent to a p-value of 0.05, and a larger −log₁₀P value equates to a smaller p-value and vice versa.