JTO: KRAS mutation, STK11 and KEAP1 mutations in lung adenocarcinoma significantly reduce immune efficacy

Immunochecklist inhibitors (ICIs) have significantly prolonged survival in lung cancer patients, but the benefits of metastatic non-small cell lung cancer (NSCLC) are limited
.
PD-L1 expression and high TMB are associated with immunotherapy benefits, but it is still difficult to distinguish the beneficial population, and other biomarkers that predict efficacy and drug resistance are urgently needed to optimize treatment strategies
.

In patients with lung adenocarcinoma (LUAD) with positive driver genes, the proportion of KRAS mutations is large, and STK11 and/or KEAP1 co-mutations, as an important subset of KRAS mutated lung cancers, have unique biological characteristics and therapeutic sensitivity
.
The STK11 gene regulates a variety of cellular functions including metabolism, growth, and polarity; About 15% of lung adenocarcinomas have STK11 deletion, which is related to lack of PD-L1 expression, tumor-invasive cytotoxic CD8+ T lymphopenia, and mediates ICI treatment resistance in patients with KRAS mutations
.
KEAP1 is a negative regulator of Nrf2, which can indirectly affect oxidative damage reactions
.
About 20% of patients with non-small cell lung cancer have KEAP1 deletion, which is related
to the immunosuppressive microenvironment characterized by reduced infiltration of CD8+ T cells and NK cells in mouse models.
However, in patients with advanced lung adenocarcinoma, the correlation between KEAP1 deletion and immune efficacy is controversial
.

Since STK11 and KEAP1 mutations often occur co-existing in NSCLC, this study sought to determine whether individual gene mutations independently affect immunotherapy outcomes and to understand whether this effect has the same mechanism
of action in KRAS mutations as well as in KRAS wild-type patients.

Research methods

Studies included two separate cohorts (Dana-Farber Cancer Institute and Massachusetts General Hospital [DFCI/MGH cohort] and Memorial Sloan Kettering Cancer Center and MD Anderson Cancer [MSKCC/MDACC cohort]) with whole genome sequencing data
.

Research results

A total of 1261 patients with advanced lung adenocarcinoma treated with PD-(L)1 inhibitors were included, of which 620 (49.
2%) were from the DFCI/MGH cohort and 641 (50.
8%) were from the DFCI/MGH cohort
.
The co-mutation rates of KRAS/STK11, KRAS/KEAP1 and STK11/KEAP1 were 10.
9% (138/1261), 8.
4% (101/1202) and 9.
4% (113/1202),
respectively.

First, the effect of KRAS, STK11, and KEAP1 mutation states on PD-L1 expression and TMB

1.
When stratified by KRAS status, PD-L1 expression was significantly reduced in patients with STK11 mutation, regardless of KRAS mutation or not; However, KEAP1 mutation was only associated with a decrease in PD-L1 expression in patients with KRAS mutation, and had no effect on KRAS wild type (Figure 1A-B).

Figure 1: PDL1 expression and TMB in different cases

When stratified by TMB status, STK11 mutations and KEAP1 mutations only had higher TMB in patients with KRAS mutations, while no difference was observed in the KRAS wild type (Figure 1C-D).

Second, the effect of STK11/KEAP1 mutation status on the clinical prognosis of KRAS mutation/wild patients receiving PD-1 inhibitor therapy

1.
Patients with KRAS/STK11 co-mutations, ORR, mPFS, and mOS were worse, but did not affect KRAS wild-type patients (Figure 2A-B, Figure 3).

STK11 mutation is an independent predictor
of poor immunotherapy PFS (HR1.
46, P=0.
01) and OS (HR 1.
73, P=0.
002).
In addition, regardless of PD-L1 expression (<1%, 1-49%, and ≥50%), KRAS/STK11 co-mutations were less
effective in immunotherapy.
The same is true
for three common mutations in KRAS (G12C/V/D).

Figure 2: ORR for immunotherapy in patients with STK11/KEAP1 mutations depending on KRAS status

2.
In patients with KRAS/KEAP1 co-mutation, the efficacy of immunotherapy was significantly reduced, but it did not affect KRAS wild-type patients (Figure 2C-D, Figure 4).

KEAP1 mutation is an independent predictor
of poor immunotherapy PFS (HR1.
46, P=0.
01) and OS (HR 2.
44, P<0.
0001).
In addition, for patients with PD-L1 expression < 1% and 1-49%, KRAS/KEAP1 co-mutation immunotherapy was less
effective.
The same is true
for three common mutations in KRAS (G12C/V/D).

Left, Figure 3.
According to different KRAS states, patients with STK11 mutations used immunotherapy PFS and OS; Right, Figure 4.
According to different KRAS states, patients with KEAP1 mutations use immunotherapy PFS and OS
.

3.
In the TCGA database, STK11 and KEAP1 mutations do not affect DFS and OS
.
In addition, STK11 and KEAP1 mutations in the DFCl database significantly reduced the efficacy of first-line platinum-based chemotherapy (ORR, PFS), but did not affect KRAS wild-type patients
.

4.
Patients with EGFR mutations or ALK rearrangements, as well as lung adenocarcinoma in never-smokers, are often suboptimal
for immunotherapy.
After excluding EGFR/ALK-positive and never-smoker patients, STK11 and KEAP1 mutations did not affect KRAS wild-type patients
.

5.
Because STK11 and KEAP1 mutations occur at the same time, whether they are independent predictors
is studied.
In KEAP1 wild-type patients, KRAS/STK11 mutations were found to significantly reduce ORR and mPFS shorter.
In STK11 wild-type patients, KRAS/KEAP1 mutations were found to not affect the ORR of immunotherapy, but significantly reduced mPFS and mOS
.
STK11 and KEAP1 mutations have been shown to be independent predictors of immune efficacy, and are less
effective when co-mutated.

Figure 5.
KRAS mutations, ORR, PFS, OS in patients with co-mutations with STK11/KEAP1

Third, gene ontology analysis showed that STK11 and KEAP1 mutations had different transcriptomic characteristics according to the KRAS mutation status

RNA sequencing data from 513 lung adenocarcinoma patients in TCGA database were analyzed and stratified
according to KRAS/STK11 and KRAS/KEAP1 co-mutation states.
Compared with KRAS mutation/STK11 wild type, 13 pathways involved in immune-mediated processes in KRAS mutation/STK11 mutation are significantly downregulated (Figure 6A).

In patients with KRAS mutations/KEAP mutations, downregulation involving 11 immune-related pathways was found (Figure 6B).

Cell type enrichment analysis showed that STK11 and KEAP1 mutant tumors had different immunophenotypes according to KRAS mutation status

Compared with patients with KRAS mutation/STK11 mutation, patients with KRAS mutation/STK11 wild-type had significant enrichment of six types of immune cells, including M1 macrophages, M2 macrophages, granulocytes, progenitor cells, CD4-positive effector memory cells, and B cells
.
Similarly, compared with patients with KRAS mutation and KEAP1 mutation at the same time, patients with KRAS mutation/KEAP1 wild-type tumors have CD8-positive T cells, memory T cells, naïve T cells, and B cells
.
Regardless of STK11 and KEAP1 gene status, this difference was not observed
in KRAS wild-type patients.

Summary

1.
This study confirmed that common mutations of STK11 and KEAP1 are important subtypes of KRAS mutated lung adenocarcinoma, which have unique immune characteristics and poor prognosis after immunotherapy, but have no effect in
KRAS wild-type patients.
In addition, this study found that patients with KRAS mutations and STK11 or KEAP1 mutations had a worse prognosis with platinum-based chemotherapy, which may have more than just immunotherapy predictive effects
.

2.
The effective rate of KRAS G12C inhibitor is about 35% ~ 45%; In addition, preclinical data show that KRAS G12C inhibition can reactivate anti-tumor immunity
through CD8-positive T cells, macrophages and dendritic cells.
The above suggests that KRAS inhibitors may work synergistically with immune checkpoint inhibitors
.
Currently, the Phase I/II trial of "Sotorasib and Adagrasib in combination with pembrolizumab" in patients with advanced NSCLC with KRAS G12C mutations is underway (NCT03600883, NCT04613596).

References

Ricciuti B, Arbour KC, Lin JJ, et al.
Diminished Efficacy of Programmed Death-(Ligand)1 Inhibition in STK11- and KEAP1-Mutant Lung Adenocarcinoma Is Affected by KRAS Mutation Status.
J Thorac Oncol.
2022 Mar; 17(3):399-410.
doi: 10.
1016/j.
jtho.
2021.
10.
013.