A new study published in Nature Cancer has validated the ORACLE signature as a reliable prognostic tool for lung adenocarcinoma (LUAD). The research, part of the TRACERx study, demonstrates ORACLE's ability to predict overall survival, identify metastatic potential, and delineate chemosensitive cells in early-stage LUAD patients. This could refine treatment strategies and improve patient outcomes.
Prospective Validation of ORACLE in LUAD
The TRACERx study, a prospective observational cohort study, utilized multiregion RNA sequencing data from 158 patients with stage I-III LUAD to validate the ORACLE signature. The study excluded patients profiled in a previous study to ensure an independent validation cohort. ORACLE risk scores were determined using predefined model coefficients and risk-score cutoffs.
Benchmarking Tumor Sampling Bias
ORACLE's tumor sampling bias was prospectively assessed and benchmarked against six comparable prognostic signatures. The results indicated that ORACLE exhibited less discordant risk classification (19%) compared to other signatures (25-44%). Furthermore, ORACLE achieved a high area under the curve (AUC) value of 0.76 in hierarchical clustering, suggesting more concordant classification of regions at the patient level. The genes comprising ORACLE also exhibited the lowest median value (0.36) for intratumor expression variability, indicating greater stability in expression across tumor regions. ORACLE reached a stable risk-score estimate at 1.3 biopsies, suggesting it yields a more stable estimate from a single tumor biopsy.
Survival Analysis and Clinical Significance
The study found a clear association between ORACLE risk class and overall survival (OS). Patients with concordant-high risk had a hazard ratio (HR) of 2.2 (95% CI 1.2–3.9) compared to concordant-low risk, while those with discordant risk had an HR of 2.5 (95% CI 1.3–4.9), P = 0.0034. After adjusting for clinicopathological risk factors, the ORACLE risk score remained significantly associated with OS (HR-adj 2.27 (95% CI 1.3–3.9), P = 0.004).
In patients with stage I LUAD, ORACLE risk classes showed a significant association with OS (log-rank P = 0.003), whereas tumor substaging criteria were not prognostically informative (log-rank P = 0.43). The association between ORACLE risk score and OS in the stage I subgroup remained significant (HR-adj 5.48 (95% CI 1.6–18.8), P = 0.007) when adjusted for clinicopathological risk factors. A meta-analysis of four microarray datasets from other institutions further validated ORACLE risk score's significant association with survival outcome in the stage I subgroup (HR 3.4 (95% CI 2.2–5.4), P = 2.8 × 10−5).
ORACLE as a Biomarker of Invasive and Metastatic Potential
ORACLE risk scores were significantly higher in metastatic samples, suggesting its potential as a signature for metastatic potential. The study found a significant association between ORACLE risk class and lung-cancer-specific survival (P = 0.011). In patients with stage I disease, ORACLE risk score was also a better predictor of lung-cancer-specific survival (AUROC 0.71) compared with other prognostic signatures.
Analysis of ORACLE risk scores across histological stages revealed an increase in expression from normal to metaplasia (linear mixed-effects model P = 0.0083). Seeding regions displayed significantly higher ORACLE risk scores than nonseeding regions (linear mixed-effects model P = 0.03). A significant association was found between ORACLE risk class and disease-free survival (DFS) (P = 0.015).
ORACLE Delineates Chemosensitive Cells
In vitro drug screen data and exploratory clinical data suggest that ORACLE high-risk LUAD tumors may be sensitive to platinum chemotherapy agents. Cisplatin was significantly correlated with efficacy in ORACLE high-risk cell lines (P = 0.045, Spearman coefficient 0.33). In the non-adjuvant-treated subgroup, a significant difference in OS rates was observed between ORACLE concordant-high risk patients (5-year OS rate 36%) and concordant-low risk patients (5-year OS rate 70%) (Cox regression P = 0.0001, HR 4.0 (95% CI 1.9–8.3)). By contrast, in the adjuvant-treated subgroup, there was no difference in OS rates between ORACLE concordant-high risk patients (5-year OS rate 69%) and concordant-low risk patients (5-year OS rate 60%) (Cox regression P = 0.8, HR 0.9 (95% CI 0.3–2.5)).
ORACLE as a Summary Metric of Lung Cancer Evolution
Tumor stage III (P = 0.002) and Ki67 (P = 0.0009) were significantly associated with ORACLE risk scores. The mean ORACLE risk score per tumor significantly correlated with SCNA-ITH (P = 0.02), FLOH (P = 0.01) and the number of clonal driver mutations (P = 0.009). ORACLE high-risk tumor regions were enriched in clonal mutations occurring in eight driver genes (PTPRB, TP53, MGA, KEAP1, SETD2, NOTCH2, ARID1A and NRAS) and depleted in tumor regions with clonal mutations of EGFR or STK11 genes.
Multivariable analysis showed that ORACLE (P = 0.008, HR 2.06), STAS (P = 0.023, HR 2.2) and preoperative ctDNA (P = 0.025, HR 2.27) remained significantly associated with OS. ORACLE risk score was responsible for the greatest variance in OS outcomes in the first year after LUAD diagnosis (PVE 16.7%) and remained informative alongside ctDNA and STAS over a 5-year follow-up period.
Implications for Clinical Practice
The validation of the ORACLE signature provides clinicians with a powerful tool to stratify patients with early-stage LUAD, predict their likelihood of survival, and guide treatment decisions. Its ability to identify chemosensitive tumors may help optimize the use of adjuvant chemotherapy, while its association with metastatic potential could inform surveillance strategies. The ORACLE signature represents a significant advancement in personalized medicine for lung cancer.
