Genetic alterations affect immune contexture of non-small cell lung cancer: Ukrainian study

Abstract

Introduction: Although the role of various genetic alterations was highlighted among factors affecting the response to immunotherapy in non-small cell lung cancer (NSCLC), the relations between oncogenic driver variants and changes in the cancer immunity cycle are still unclear.

Aim: The study aimed to discover the links between the molecular and immune context of NSCLC.

Materials and methods: This cohort study included 254 cases of NSCLC (193 Lung Adenocarcinomas) (LUAD; 76%), and 61 squamous cell carcinomas (SCC; 24%), with pathology reports and next-generation sequencing (NGS) data available. First, the rate and spectrum of genetic alterations were assessed in the Ukrainian cohort. Second, we uncovered the relationship between the oncogenic driver mutations and PD-L1 expression in NSCLC. Finally, T-cytotoxic lymphocytes (CD8⁺) and tumor-associated macrophages (CD163⁺) were evaluated in samples with EGFR and KRAS mutations, ALK rearrangements and LUAD with no genetic findings. Immune desert, immune excluded and inflamed types of tumor immune microenvironment (TME) were defined according to the cancer immunity cycle.

Results: More than half (52%) of the observed NSCLC cases harbored single (48.03%) or concomitant (3.94%) genetic alterations in oncogenes. The Ukrainian cohort demonstrated a high rate of EGFR (18.5%) and ALK rearrangements (9.4%) with a relatively moderate frequency of KRAS mutations (16.9%). NSCLC tumors with alterations in EGFR and ALK demonstrated a high incidence of PD-L1 expression and specific immune contexture. The number of CD8⁺ cells varied significantly between oncogene-driven and wild-type LUAD (p = 0.019). Non-oncogene-addicted NSCLC demonstrated the prevalence of Inflamed TME rich in CD163⁺ macrophages. In contrast, over half of EGFR mutant LUAD cases possessed immune desert TME type, while ALK-rearranged and KRAS mutant NSCLC showed mostly immune excluded TME.

Conclusion: The high rate of PD-L1 expression in NSCLC driven by EGFR and ALK alterations was accompanied by a prevalence of low immunogenicity with a shift toward ID TME in EGFR mutant tumors and IE TME in ALK-rearranged and KRAS mutant NSCLC. Further discovery of mechanisms affecting tumor immune contexture is needed for tailoring patient management in line with particular mechanisms of immune evasion.

Keywords: adenocarcinoma; cancer immunity cycle; genetic alterations; immune contexture; non-small cell lung cancer; oncogenes.

Figure 1

The incidence and spectrum of genetic alterations in NSCLC. (A) The frequency of genetic alterations in the whole Ukrainian cohort of patients with NSCLC. (B) The spectrum and rate of genetic findings in LUAD. (C) The spectrum and rate of genetic findings in SCC. LUAD, lung adenocarcinoma; SCC, squamous cell carcinoma.

Figure 2

The rate of PD-L1 expression in oncogene-addicted and non-oncogene-addicted NSCLC. Tumors with genetic alterations in EGFR and ALK demonstrated were prone to PD-L1 expression that reached 85–87% of all carcinomas. In contrast, non-oncogene addicted NSCLC demonstrated a significantly lower rate of PD-L1 expression.

Figure 3

Density of CD8⁺ and CD163⁺ immune cell presence within tumor and tumor stroma of wild-type (WT), EGFR mutant, ALK-rearranged, and KRAS mutant LUAD. Panels (A,B) demonstrate the number of CD8⁺ cells within the tumor and in the peritumor stroma, respectively. Panels (C,D) showed the amount of CD163⁺ macrophages within the tumor and in the peritumor stroma, respectively. Oncogene-addicted LUAD demonstrated a significantly lower number of CD8⁺ cells infiltrating the tumor.

Figure 4

Prevalence of immune phenotypes in tumors with no detected genetic variants (wild-type, WT), EGFR mutant (EGFRm), ALK-rearranged (ALKr), and KRAS mutant LUAD (KRASm).

Figure 5

Immune cells in LUAD of with different immune phenotype and their interplay with PD-L1 expression. Panels (A,C) demonstrate the count of CD8⁺ cells and CD163 macrophages in LUAD of the immune desert (ID), immune excluded (IE) and Inflamed (INF) type of tumor microenvironment. Panels (B,D) show the link between PD-L1 expression and density of CD8⁺ cells and CD163⁺ macrophages. Positive tumor PD-L1 status is related to a high density of CD163⁺ cells, but not CD8⁺ cells.