Integrating the 40-Gene Expression Profile (40-GEP) Test Improves Metastatic Risk-Stratification Within Clinically Relevant Subgroups of High-Risk Cutaneous Squamous Cell Carcinoma (cSCC) Patients

Abstract

Introduction: The validated 40-gene expression profile (40-GEP) test independently stratifies risk of regional or distant metastasis for cutaneous squamous cell carcinoma (cSCC) tumors with high-risk clinicopathologic features. This study evaluated the stratification of risk by the 40-GEP test in a large cohort of tumors with one or more high-risk factors and in clinically relevant subgroups, including tumors within National Comprehensive Cancer Network (NCCN) high- and very-high-risk groups, lower-stage BWH T1 and T2a tumors, and patients > 65 years old.

Methods: This multicenter (n = 58) performance study of the 40-GEP included 897 patients. Kaplan-Meier analyses were performed to assess risk stratification profiles for 40-GEP Class 1 (low), Class 2A (higher) and Class 2B (highest) risk groups, while nested Cox regression models were used to compare risk prediction of clinicopathologic risk classification systems versus risk classification systems in combination with 40-GEP.

Results: Patients classified as 40-GEP Class 1, Class 2A, or Class 2B had significantly different metastatic risk profiles (p < 0.0001). Integrating 40-GEP results into models with individual clinicopathologic risk factors or risk classification systems (Brigham and Women's Hospital, American Joint Committee on Cancer Staging Manual, 8th Edition) and NCCN demonstrated significant improvement in accuracy for prediction of metastatic events (ANOVA for model deviance, p < 0.0001 for all models).

Conclusion: The 40-GEP test demonstrates accurate, independent, clinically actionable stratification of metastatic risk and improves predictive accuracy when integrated into risk classification systems. The improved accuracy of risk assessment when including tumor biology via the 40-GEP test ensures more risk-aligned, personalized patient management decisions.

Keywords: 40-GEP; Cutaneous squamous cell carcinoma; Metastasis; Prognostic; Risk assessment.

Fig 1

Flow chart describing final patient cohort and attrition due to study eligibility. *Did not meet protocol inclusion criteria, lacked sufficient material to be run under clinical standard operating procedures, did not meet clinical testing inclusion criteria. ART adjuvant radiation therapy

Fig 2

Kaplan-Meier plot based on metastasis-free survival (MFS) for the combined cohort, demonstrating significant stratification by 40-GEP results (log-rank test). The table below the plot indicates the number of patients at risk annually for each 40-GEP risk class. The bottom table demonstrates 3-year MFS rates for each 40-GEP class and associated metastatic event rates, in addition to overall survival metrics for the cohort

Fig 3

Kaplan-Meier survival analysis subset by the National Comprehensive Cancer Network (NCCN, v1.2024) risk classification system demonstrated statistically significant 3-year metastasis-free survival (MFS) between all 40-GEP classes. A NCCN high risk, B NCCN very high risk; Tables as described in Fig. 2, p values indicate log-rank tests

Fig 4

Kaplan-Meier survival analysis of Brigham and Women’s Hospital (BWH) lower risk stages demonstrated statistically significant 3-year metastasis-free survival (MFS) between all 40-GEP classes. (A) BWH T1; (B) BWH T2a; Tables as described in Fig. 2, p values indicate log-rank tests

Fig 5

Kaplan-Meier survival analysis of the ≥ 65 (25th quartile) and ≥ 80 (75th quartile) years of age at diagnosis subsets demonstrated statistically significant 3-year metastasis-free survival (MFS) between all 40-GEP classes. Tables as described in Fig. 2; p value indicates log-rank tests