Aims: Non-small-cell lung cancer (NSCLC) comprises 85-90% of all lung cancers, with the highest burden of mortality worldwide. One of the major reasons for this is its heterogeneity which harbors multiple histological subtypes predominantly being lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Therefore, our primary aim is to stratify the patient transcriptomic data into distinct molecular profiles that will manifest the association between subtypes and functional categories. Furthermore, underlining the differences within the complex TME to study the distinguished immune-cell atlas of LUAD and LUSC, and their crosstalk with the tumor cells.
Methods: To elucidate the nature of interactions between tumor cells and the TME, we exploited the transcriptome of 300 early stages (Ib-IIIa) NSCLC patients recruited in the prospective clinical trial PROMOLE study. With the help of a clustering approach, initially we performed a molecular-based virtual stratification/dissection on the NSCLC patients. Next, to elucidate the relative cell-type abundance, a deconvolution approach was applied to identify the possibility of tumor infiltrating immune cells within these subgroups. Immunohistochemistry (IHC) was then used to substantiate these predictions on tumor cells.
Results: The resulting subgroups of LUADs and LUSCs are biologically well-characterized by mutational and gene expression profiles. Cell-type abundance approach identified samples which are enriched with tumor infiltrating immune cells like Neutrophils, Tcells, macrophages, etc. These findings were positively confirmed by IHC with multiple cell markers such as MPO, CD4, CD8, CD68, etc. Integrating these two results highlighted the proportion of tumor immune microenvironment (TiME) in the two different sub-populations along with shedding some light on the crosstalk happening between different cancer-/immune- cells.
Discussion and conclusion: The in-silico predictions on bulk RNA data by virtual micro-dissection, distinguished the two distinct NSCLC subtypes, each associated with clinical and molecular features. Furthermore, the immune cells infiltration suggests a possible role of infiltrating tumor immune cells with the prognosis of patients. Our analysis successfully performed an intra-sample and inter-sample comparison, which can unveil new prognostic markers that can provide relevant information for cancer immunotherapy.