Differential association of STK11 and TP53 with KRAS mutation-associated gene expression, proliferation and immune surveillance in lung adenocarcinoma

Abstract

While mutations in the KRAS oncogene are among the most prevalent in human cancer, there are few successful treatments to target these tumors. It is also likely that heterogeneity in KRAS-mutant tumor biology significantly contributes to the response to therapy. We hypothesized that the presence of commonly co-occurring mutations in STK11 and TP53 tumor suppressors may represent a significant source of heterogeneity in KRAS-mutant tumors. To address this, we utilized a large cohort of resected tumors from 442 lung adenocarcinoma patients with data including annotation of prevalent driver mutations (KRAS and EGFR) and tumor suppressor mutations (STK11 and TP53), microarray-based gene expression and clinical covariates, including overall survival (OS). Specifically, we determined impact of STK11 and TP53 mutations on a new KRAS mutation-associated gene expression signature as well as previously defined signatures of tumor cell proliferation and immune surveillance responses. Interestingly, STK11, but not TP53 mutations, were associated with highly elevated expression of KRAS mutation-associated genes. Mutations in TP53 and STK11 also impacted tumor biology regardless of KRAS status, with TP53 strongly associated with enhanced proliferation and STK11 with suppression of immune surveillance. These findings illustrate the remarkably distinct ways through which tumor suppressor mutations may contribute to heterogeneity in KRAS-mutant tumor biology. In addition, these studies point to novel associations between gene mutations and immune surveillance that could impact the response to immunotherapy.

Fig. 1. Co-occurring and mutually exclusive mutations in KRAS, STK11, TP53 and EGFR in 442 human lung adenocarcinoma samples

(a) Tumors with specific mutations are indicted in red while tumors without mutations are in green. To demonstrate co-occurring and exclusive mutations, the samples were sorted by KRAS mutations, then SKT11 mutations, then TP53 mutations, and then EGFR mutations. (b–e) Association of oncogene and tumor suppressor gene mutations with OS among stage I lung adenocarcinoma patients (n=265). Kaplan–Meier survival curves by mutation status of (b) KRAS, (c) STK11, (d) TP53, and (e) EGFR are shown. A two-sided log-rank test was used to assess statistically significant differences by mutational status. The number of patients at risk is listed below the survival curves. Additional methodology is provided in Supplemental Information.

Fig. 2. Impact of STK11 and TP53 mutations on KRAS mutation-associated gene expression

(ac) Boxplots indicating KRAS mutation-associated (RAS de novo) signature activity (PC1) within each gene group (a) KRAS, (b) STK11, and (c) TP53. T-test was used to determine significance in difference in signature activity between mut and wt groups indicated. Sample size (n), mean and standard deviation (std) is indicated on top of each figure. (d) Boxplots and (e) pairwise comparison plots indicating RAS de novo signature activity in indicated co-occurring and exclusive mutations in KRAS and STK11. ANOVA was used to determine overall significant difference in RAS de novo signature activity among indicated groups and Tukey honest significant difference method was used to adjust for p value for pairwise comparison. (f) Boxplots and (g) pairwise comparison plots indicating RAS de novo signature activity in indicated co-occurring and exclusive mutations in KRAS and TP53. Additional methodology is provided in Supplemental Information.

Fig. 3. Distinct association of TP53 mutations with tumor proliferative responses

(a–b) Boxplots indicating MR signature activity (PC1) within each gene group (a) KRAS, (b) STK11, and (c) TP53. T-test was used to determine significance in difference in MR activity between mut and wt groups indicated. Sample size (n), mean and standard deviation (std) is indicated on top of each figure. (d) Boxplots and (e) pairwise comparison plots indicating MR signature activity in indicated co-occurring and exclusive mutations in KRAS and STK11. ANOVA was used to determine overall significant difference in MR activity among indicated groups and Tukey honest significant difference method was used to adjust for p value for pairwise comparison. (f) Boxplots and (g) pairwise comparison plots indicating MR signature activity in indicated co-occurring and exclusive mutations in KRAS and TP53.

Fig. 4. Suppression of immune surveillance in STK11 mutant tumors

(a–c) Boxplots indicating NF-κB signature activity (PC1) within each gene group (a) KRAS, (b) STK11, and (c) TP53. T-test was used to determine significance in difference in NF-κB activity between mut and wt groups indicated. Sample size (n), mean and standard deviation (std) is indicated on top of each figure. (d) Boxplots and (e) pairwise comparison plots indicating NF-κB signature activity in indicated co-occurring and exclusive mutations in KRAS and STK11. ANOVA was used to determine overall significant difference in NF-κB activity among indicated groups and Tukey honest significant difference method was used to adjust for p value for pairwise comparison. (f) Boxplots and (g) pairwise comparison plots indicating NF-κB signature activity in indicated co-occurring and exclusive mutations in KRAS and TP53. (h) Boxplots indicating TCR gene expression PC1 activity. T-test was used to determine significance in difference in TCR expression between indicated mut and wt groups.