50 Circulating genomic biomarkers predict chemoradiotherapy resistance and immunotherapy response in locally advanced non-small cell lung cancer

Background

Efficacy of curative-intent chemoradiotherapy (CRT) and consolidation immune checkpoint inhibitor (ICI) is heterogenous in unresectable locally advanced non-small-cell lung cancer (LA-NSCLC). Effective biomarkers to early identify resistance to CRT and guide risk-adaptive consolidation immunotherapy are urgently needed. The clinical value of STK11 (LKB1) and KEAP1 alterations in NSCLC remains controversial, since patients with these theoretically resistance-related mutations exhibited favorable ICI benefits.

Methods

In this prospective cohort trial (NCT06287320), patients with unresectable stage II-III NSCLC were assigned to the CRT or CRT plus consolidation ICI groups. Peripheral blood samples were collected at longitudinal landmark timepoints, including pretreatment, during-CRT, post-CRT, and at disease progression, to profile circulating tumor DNA (ctDNA) dynamics and genomic features. Blood-based tumor genotyping was performed using pretreatment plasma and leukocytes. An independent cohort of ctDNA molecular residual disease (MRD) testing from 87 LA-NSCLC patients receiving CRT alone or CRT + consolidation ICI was employed for external validation. Whole genome or whole exome sequencing from 421 LA-NSCLC patients and RNA-sequencing data from 1,149 patients were used for tumor tissue-based validation and mechanism exploration.

Results

A total of 239 blood samples from 73 patients, including 36 with CRT and 37 with CRT plus ICI, were analyzed. Pretreatment blood-based STK11/KEAP1 alterations were associated with poorer prognosis and CRT resistance but additional survival benefits from consolidation immunotherapy. In the ctDNA-MRD validation cohort, STK11/KEAP1 mutations could early identify inferior outcomes with CRT but significantly favorable consolidation ICI responses. Tumor tissue genomic profiling confirmed STK11/KEAP1 alterations were poor prognostic factors correlated with resistance to definitive CRT. RNA sequencing revealed STK11/KEAP1-mutated tumors were characterized by immunosuppressive phenotype before treatment, particularly strikingly decreased Th17 cells in the tumor microenvironment through IL-17 signaling downregulation, which might result in impaired anti-tumor immune responses to upfront treatments but improved efficacy of consolidation ICI by activating local anti-tumor immunity after definitive radiotherapy. Although patients with undetectable ctDNA MRD post CRT had excellent outcomes irrespective of consolidation ICI, the subgroup with STK11/KEAP1 alterations effectively benefited from further ICI therapy, highlighting baseline STK11/KEAP1 as a potential remedy for false negatives generated by individual ctDNA-MRD detection.

Conclusions

STK11/KEAP1 alterations were correlated with poor prognosis and resistance to upfront CRT, but identified more benefits from consolidation ICI therapy. Considering genomic features in the context of liquid biopsy biomarkers could facilitate more personalized treatment decisions.

Acknowledgements

We are grateful to all patients and their families who participated in this study.

Trial Registration

This biomarker study was and registered at ClinicalTrials.gov (NCT06287320).

Ethics Approval

This study was approved by the Ethics Committee of Chinese Academy of Medical Sciences (No. 19/098-1883).

Consent

Written informed consent was obtained from the patient for publication of this abstract and any accompanying images. A copy of the written consent is available for review by the Editor of this journal.