Integrating gene expression profiling into NCCN high-risk cutaneous squamous cell carcinoma management recommendations: impact on patient management

Abstract

Objective: To integrate gene expression profiling into the management of high-risk cutaneous squamous cell carcinoma (cSCC) within the National Comprehensive Cancer Network (NCCN) guidelines to improve risk-aligned management recommendations.

Methods: A cohort of 300 NCCN-defined high-risk cSCC patients, along with the American Joint Committee on Cancer (AJCC) T stage, Brigham and Women’s Hospital (BWH) T stage, and known patient outcomes were analyzed. Risk classifications using a validated 40-gene expression profile (40-GEP) test and T stage were applied to NCCN patient management guidelines. Risk-directed patient management recommendations within the NCCN guidelines framework were aligned based on risk for metastasis.

Results: Of the 300 NCCN high-risk cSCC patients, 159 (53.0%) were 40-GEP Class 1 and AJCC T1-T2, and 173 (57.7%) were Class 1 and BWH T1-2a, indicating low risk for metastasis and, thereby, suggesting low management intensity. The 40-GEP integration suggested high intensity management for only 24 (8.0%) patients (all Class 2B), and moderate intensity management for the remainder of the cohort.

Conclusions: The 40-GEP test can be integrated within existing NCCN guideline recommendations for managing cSCC patients to help refine risk-directed management decisions. Integration of the 40-GEP test would allow >50% of this NCCN-defined high-risk cohort to be managed with the lowest intensity recommendations within the broad NCCN guidelines. High intensity management was deemed risk-appropriate for a small subpopulation (8.0%). This study demonstrates that the 40-GEP test, in combination with T stage, has clinical utility to impact patient management decisions in NCCN high-risk cSCC for improving risk-aligned management within the NCCN guidelines framework.

Keywords:

• Cutaneous squamous cell carcinoma
• metastasis risk
• gene expression profile
• tumor biology
• patient management

This article is related to:

Impact of a prognostic 40-gene expression profiling test on clinical management decisions for high-risk cutaneous squamous cell carcinoma

Introduction

Cutaneous squamous cell carcinoma (cSCC) is the second most common form of skin cancer after basal cell carcinoma^1–4. It occurs in approximately one million people in the U.S. and the incidence is rising, partly due to enhanced detection methods and an aging population^1,4–8. Overall, approximately 6% of cSCC patients develop regional or distant metastatic lesions and survival rates are low for those who do develop metastasis^5,7,9–13. The number of deaths from cSCC, a large proportion of which are preceded by metastasis, has been estimated to rival that from melanoma^4,14. Therefore, accurate prediction of risk for metastasis is essential for optimal patient management and, ultimately, to potentially improve outcomes.

National Comprehensive Cancer Network (NCCN) guidelines outline management pathways for low- and high-risk cSCC patients. Within this framework, the NCCN management recommendations are broad for patients who have a low likelihood of recurrence and/or metastasis, as are recommendations for cSCC patients considered high risk for developing recurrence and/or metastasis⁵. Risk stratification and staging systems for cSCC include NCCN guidelines criteria, the American Joint Committee on Cancer (AJCC) Cancer Staging Manual (8th Edition, AJCC8), and the Brigham and Women’s Hospital (BWH) tumor classification system^5,15–19. These systems are based on clinical and pathological features; however, they are specifically limited in their ability to predict adverse events such as metastasis (i.e. have low positive predictive value [PPV] for metastasis)^17–21 and pose a challenge to implementing risk-directed patient management. Patients with cSCC would benefit from improved prognostic tools for determining which patients currently considered clinicopathologically “high risk” are truly at low risk for metastasis, which patients should consider procedures to detect nodal or distant disease (e.g. nodal biopsy versus imaging versus clinical examination only), and which should consider or be recommended adjuvant therapeutic intervention to reduce risk for recurrence and metastasis (e.g. adjuvant radiation, systemic therapy, additional surgery, and/or clinical trial enrollment). Given that risk classifications guide treatment plans, improved prognostic tools would enhance shared decision-making between physicians and their patients. Ultimately, the goal is early intervention for individuals who are likely to develop metastasis, and avoidance of unnecessary invasive or costly procedures for those who are at lower risk for developing metastasis.

A 40-gene expression profile (40-GEP) test using archival, formalin-fixed paraffin-embedded (FFPE), primary cSCC tissue was recently developed and validated²². This test stratifies clinicopathologically-confirmed cSCC tumors into three risk groups based on low (Class 1), high (Class 2A), and highest (Class 2B) risk for regional or distant metastasis at 3 years after diagnosis²². A substantially higher PPV (60.0%) was found for the 40-GEP test for Class 2B relative to that found for the AJCC8 (32.8%) and BWH (35.1%) staging systems, while maintaining a negative predictive value (NPV) of approximately 90.0% (which is similar to that of the AJCC8 and BWH systems)²². The primary goal of developing and validating the 40-GEP test was to improve metastasis risk prediction. Similar prognostic tests for cutaneous melanoma^23–26, uveal melanoma²⁷, breast cancer^28–30, prostate cancer^31,32, and thyroid cancer^33,34 have demonstrated clinical utility for guiding patient management decisions^35–39.

The current study aimed to refine risk-directed patient management recommendations by integrating 40-GEP test results from NCCN-defined high-risk patients within the broad framework of the NCCN guidelines²². Herein, we demonstrate that integration of this molecular prognostic tool, which has higher PPV (and similar NPV) relative to current staging systems, identified >50% of the NCCN-defined high-risk cohort as low risk for metastasis (40-GEP Class 1 and low-risk T stage), with metastasis rates similar to rates in clinicopathologic low-risk cases. This suggests that this subgroup could be managed at the lower end of intensity within the NCCN guidelines for high-risk patients. By comparison, integration of the 40-GEP test also identified a smaller subgroup of patients (8% of the high-risk cohort) as the highest risk for metastasis (Class 2B tumor). This would warrant more aggressive intervention aligned with management at the higher end of intensity within the NCCN guidelines for high-risk patients, thereby achieving risk-appropriate allocation of surgical, imaging, and therapeutic resources. In all, integrating the 40-GEP test within risk-directed NCCN guidelines for patient management resulted in more personalized, risk-aligned treatment recommendations and potential improvement in net health outcomes.

Materials and methods

The 40-GEP test and data from the clinical validation cohort

Recently validated and reported by Wysong et al.²², the 40-GEP test is an RT-PCR-based, gene expression profile (GEP), prognostic test that stratifies patients with clinicopathologically-confirmed cSCC tumors into three groups based on risk for metastasis (regional or distant) within 3 years of diagnosis: low (Class 1), high (Class 2A), and highest (Class 2B) risk. The current manuscript includes analysis of data from only those patients (n = 300) in the clinical validation cohort (described in Wysong et al.) who had high-risk cSCC per the NCCN guidelines definition. This high-risk cSCC cohort was analyzed to determine the impact of integrating the 40-GEP test into management of high-risk cSCC patients within the framework established by NCCN patient management guidelines. The following data for these high-risk cSCC patients were analyzed: metastasis risk class (40-GEP results), T stage (AJCC8 and BWH), and known patient outcomes (i.e. metastasis versus no metastasis). This high-risk cohort included only cases meeting study criteria and having one or more NCCN-defined high-risk features, as noted in Table 1. Briefly, criteria for study inclusion were pathologically-confirmed cSCC diagnosed after 1 January 2006; available FFPE primary cSCC tumor tissue; complete case report forms; and documented metastasis or minimum follow-up period of 3 years without metastasis. Study cohort demographics and clinical characteristics were monitored and underwent centralized pathology review (Table 1).

Table 1. Characteristics of the NCCN high-risk cSCC cohort (n = 300).

Feature of modeling cohort	Cases (% of cohort)
Age: median years (range)	70 (34–95)
Sex: male	219 (73%)
Immune deficient	76 (25%)
Located on H&N	201 (67%)
Tumor diameter^a: mean cm (≥2 cm)	1.85 (36%)
Tumor thickness^b: mean mm (>6 mm)	3.90 (16%)
Poorly differentiated	36 (12%)
Clark level IV/V	62 (21%)
PNI present	36 (12%)
Subcutaneous fat invasion	43 (14%)
40-GEP result
Class 1	189 (63%)
Class 2A	87 (29%)
Class 2B	24 (8%)

^a275 cases had tumor diameter reported; ^b109 cases had thickness reported.

Abbreviations. NCCN, National Comprehensive Cancer Network; H&N, head and neck; PNI, perineural invasion; GEP, gene expression profile.

Notes. NCCN high-risk criteria include tumor size ≥2 cm; tumor depth >6 mm or invasion beyond subcutaneous fat; poorly differentiated; perineural invasion; bone invasion; on ear or lip; on mask area of the face; on genitalia, hands, or feet; on forehead, scalp, cheek, or neck (size ≥10 mm); rapid growth; immunosuppression; site of prior radiation therapy or chronic inflammatory process; recurrent tumor; neurologic symptoms; high-risk subtypes (acantholytic, adenosquamous, or desmoplastic).

Statistical analysis and integration of 40-GEP results within risk-aligned management recommendations

For the NCCN-defined high-risk cohort (n = 300), the numbers of patients stratified in each 40-GEP Class and per AJCC8 and BWH T stage were analyzed. Corresponding metastasis rates for groups defined by 40-GEP Class 1, 2A, and 2B results, and by AJCC8 (T1-T2 and T3-T4) and BWH (T1-T2a and T2b-T3) T stage were categorized into risk bins of <10%, 10–49%, or ≥50% risk for metastasis, which were aligned with risk-appropriate recommendations for management intensity (low, moderate, or high, respectively). Kaplan–Meier analysis with log-rank testing was performed, as previously described²², to compare metastasis-free survival (MFS) rates of the patients across the three management intensity categories per AJCC8 or BWH T stage. A p-value of ≤ .05 was considered statistically significant.

Within the broad range of existing recommendations for high-risk cSCC patients with localized disease, NCCN management recommendations for follow-up frequency, nodal assessment (with or without imaging, biopsy, and/or neck dissection), adjuvant therapy, and clinical trials were aligned with low, moderate, and high intensity management strategies. Corresponding risk-aligned management plans within the lower, mid (moderate), and higher intensity ranges of the NCCN guidelines framework were recommended for high-risk cSCC patients.

Results

Cohort characteristics, 40-GEP risk classification, and outcomes

A 300-case cohort of NCCN-defined high-risk cSCC patients (Table 1) was analyzed to integrate the recently validated 40-GEP test into NCCN guidelines and T stage criteria for patient management to improve risk-aligned management recommendations. The 40-GEP test classifies patients into three risk groups: Class 1, Class 2A, and Class 2B, having low, high, and highest risk for metastasis at 3 years post-diagnosis, respectively. Of the 300 cases, 189 (63.0%) were Class 1, 87 (29.0%) were Class 2A, and 24 (8.0%) were Class 2B with overall metastasis rates of 9%, 21%, and 63%, respectively (Figure 1(A)). More than 50% of the cases were Class 1 and AJCC8 T1-T2 (n = 159, 53.0%) or BWH T1-T2a (n = 173, 57.7%) with metastasis rates below 10% (AJCC8, 7.5%; BWH, 8.1%) (Figure 1(A,B)). Whereas, Class 1 cases that were also AJCC8 T3-T4 or BWH T2b-T3, as well as all Class 2A cases, had metastasis rates above 10%, but lower than 50%. All Class 2B cases (8.0% of the cohort) had metastasis rates that were greater than 50%.

Figure 1. Application of 40-GEP test results to NCCN-defined high-risk status and T stage for improving risk-appropriate management of cSCC. (A) Using a cohort (n = 300) of clinicopathologically-defined cSCC patients meeting study criteria and who were NCCN-defined high risk, the 40-GEP test stratified the patients into three groups depending on risk for metastasis at 3 years post-diagnosis: low (Class 1, n = 189), high (Class 2A, n = 87), or highest (Class 2B, n = 24). Patients stratified as Class 1, 2A, and 2B had a 9%, 21%, and 63% risk for metastasis, respectively, per the 40-GEP test alone. Corresponding AJCC8 and BWH T stages and metastasis rates were analyzed. (B) Incorporation of 40-GEP Class plus AJCC8 and BWH T stages into three metastasis risk bins (<10%, 10–49%, and ≥50% risk) resulted in low, moderate, and high intensity management strategies. The 40-GEP integration demonstrates low management intensity for 53.0% (AJCC8) or 57.7% (BWH), high intensity management for 8.0%, and moderate intensity management for the remainder (39.0%, AJCC8; 34.3%, BWH) of the 300-patient cohort. (C) Metastasis-free survival (MFS) rates of patients from the cohort risk-aligned with low, moderate, or high intensity management per 40-GEP Class and AJCC8 or BWH T stage. Kaplan–Meier analysis revealed 3-year MFS rates of 92.5% for patients in the low intensity management category (both AJCC8 and BWH), 82.1% and 80.6% for those in the moderate intensity category (AJCC8 and BWH, respectively), and 41.7% for patients in the high intensity category (both AJCC8 and BWH). Statistically significant differences were found for these MFS curves for both 40-GEP Class plus AJCC8 and 40-GEP Class plus BWH T stage (p ≤ .001, log-rank).

Clinical utility of integrating the 40-GEP test

By combining the low-risk Class 1 result with AJCC8 T1-T2 stage or BWH T1-T2a stage, a 3-year metastasis rate of 7.5% (NPV, 92.5%) or 8.1% (NPV, 91.9%), respectively, was identified for this subgroup within the NCCN-defined high-risk cohort (Figure 1(A)). This metastasis rate approaches the rate reported for the general cSCC patient population (≤6% metastasis)^{7,9–11,13,17}. Of the Class 1 cases, 159 and 173 were AJCC8 T1-T2 and BWH T1-T2a, respectively, and were risk-aligned (<10% risk for metastasis) for receiving low intensity management (Figure 1(A,B)). The 40-GEP test identified a highest-risk (Class 2B) subpopulation (n = 24, 8.0%), which was risk-aligned (≥50% risk for metastasis) for receiving high intensity management (16 and 8 of the patients were AJCC8 T1-T2 and T3-T4, respectively; 17 and 7 were BWH T1-2a and T2b-T3, respectively). Of the remainder of the cohort, 64 were Class 2A/AJCC8 T1-T2 and 73 were Class 2A/BWH T1-T2a, with a risk for metastasis of 15.6% and 17.8%, respectively (Figure 1(A)). These rates are lower than that for the overall Class 2A rate for the cohort, but still more than twice that of the general cSCC patient population. Moderate intensity management was suggested for this group, as well as those patients who were Class 1 or 2A and AJCC8 T3-T4 or BWH T2b-T3 (10–49% risk for metastasis, Figure 1(A,B)).

The 40-GEP test results, when adjusted for AJCC8 or BWH T stage in this study, suggest low management intensity for 53.0% or 57.7% of the 300-patient cohort, respectively (Figure 1(B)). Integration of the 40-GEP test also suggests maintaining moderate intensity management for 39.0% (40-GEP + AJCC8) or 34.3% (40-GEP + BWH), and high intensity patient management for 8.0% of the cohort (Figure 1(B)). Kaplan–Meier analysis determined a statistically significant difference in 3-year MFS rates for the cases aligned with the low, moderate, and high-intensity management strategies (p ≤ .001, log-rank). The low management intensity group had an MFS rate of 92.5% (95% CI, 88.4–96.7% or 88.6–96.5% for 40-GEP Class plus AJCC8 or BWH staging, respectively) (Figure 1(C)). The moderate management intensity group had an MFS rate of 82.1% (95% CI, 75.4–89.3%) or 80.6% (95% CI, 73.3–88.6%) for 40-GEP Class plus AJCC8 or BWH, respectively, and the high management intensity group had an MFS rate of 41.7% (95% CI, 26.0–66.9%) for 40-GEP Class plus AJCC8 or BWH (Figure 1(C)).

Discussion

The 40-GEP test was recently reported to be an independent predictor of 3-year metastasis risk in cSCC with improved metastasis risk prediction compared to AJCC8 and BWH²². Herein, the 40-GEP test results for a cohort of 300 NCCN-defined high-risk cSCC patients were combined with T stage, and corresponding metastasis risk bins (<10%, 10–49%, and ≥50% risk) were aligned with risk-directed management intensities (low, moderate, and high intensity, respectively). Statistical analysis demonstrated significant differences in MFS rates at three years post-diagnosis (the period during which most cSCC metastases occur) for patients across the three management intensity categories when 40-GEP Class was combined with either AJCC8 or BWH T stage. Recommendations for improving risk-aligned patient management via low, moderate, and high intensity management plans were developed within the NCCN guidelines framework.

As shown in Figure 2, within the NCCN guidelines framework, low intensity management for these types of Class 1 patients would involve low frequency follow-up visits (1–2 visits/year), nodal assessments via palpation only, and avoidance of adjuvant radiation therapy (RT) or systemic therapy. Moderate intensity management based on NCCN recommendations would allow for fewer follow-up visits relative to high intensity management (Figure 2). Follow-up would include nodal palpation and consideration of imaging and/or nodal biopsy or dissection (when warranted)^5,40,41 as well as adjuvant radiation, chemotherapy, and/or immunotherapy during moderate intensity management. This would potentially result in fewer invasive procedures (less imaging, fewer nodal biopsies and dissections) and more sparing use of adjuvant therapy relative to high intensity management during which many of these procedures, including clinical trials, would be recommended (Figure 2).

Figure 2. Recommended risk-aligned cSCC patient management plans within the NCCN guidelines framework for prognostic groups based on 40-GEP Class and T stage. Risk for regional/distant metastasis is reported for 40-GEP Class and BWH T stage. *Adjustment of clinical follow-up should be based on risk per the NCCN guidelines. **Imaging, nodal biopsy, and/or neck dissection should be considered (moderate intensity management) or recommended (high intensity management) when warranted per the NCCN, American Academy of Dermatology, and Que et al.⁴¹.

This integration demonstrates the validated 40-GEP prognostic test has clinical utility for complementing current staging systems^15–17 and refining risk-appropriate pathways recommended by national guidelines⁵ for improved management of cSCC patients deemed high risk by clinicopathologic methods. The 40-GEP test provides more accurate prediction of risk for metastasis in NCCN-defined high-risk cSCC patients within three years post-diagnosis, enabling improved risk-directed management decisions for therapy and surveillance. The current study reports the value of the test to identify within an NCCN high-risk cSCC patient population: (1) low-risk patients, having metastasis rates similar to rates of the general cSCC patient population, and who could benefit from management within the lower intensity end of the spectrum of guideline recommendations, including avoiding adjuvant therapy; and (2) truly high-risk patients who may benefit from management aligned within the highest intensity end of the spectrum of existing management recommendations. The value of more accurate prognosis is the ability to have better-informed decision making for aligning low and high risk of poor outcomes with appropriate management strategies. Collectively, the 40-GEP test may, in combination with AJCC8 or BWH T stage, help refine risk-directed management of high-risk cSCC patients within the current framework of NCCN guidelines for these patients. In summary, integration of the 40-GEP test into management of high-risk cSCC could enable improved risk-aligned management for the majority of patients tested and potentially improve net health outcomes.

Conclusions

The 40-GEP test can be integrated within NCCN guideline recommendations and, in combination with T stage, may have clinical utility for impacting and improving risk-aligned cSCC patient management.

Transparency

Declaration of funding

Research for this study and writing of this manuscript were supported by Castle Biosciences, Inc.

Declaration of financial/other relationships

ASF and SMD serve as members on the advisory board for Castle Biosciences, Inc. MAH, KRC, SJK, and RWC are employees and also hold stock options at Castle Biosciences, Inc. A peer reviewer on this manuscript discloses cooperation with Castle Biosciences in research works on cutaneous squamous cell carcinoma, but they have not been implicated in this particular paper. Peer reviewers on this manuscript have received an honorarium from CMRO for their review work but have no other relevant financial relationships to disclose.

Author contributions

ASF, RWC, SJK, KRC, and SMD were involved in the conception and design, as well as analysis and interpretation of data. MAH, SJK, and RWC drafted the manuscript. ASF, MAH, LD, SJK, RWC, and SMD were involved with revising it critically for intellectual content. All authors approved the final version of the manuscript submitted and agree to be accountable for all aspects of the work.

Previous presentations

Data from this study were submitted for poster presentation at the 2020 Winter Clinical Dermatology Conference, January 17–22, 2020, and the Maui Derm for Dermatologists 2020 meeting, January 25–29, 2020.

Acknowledgements

The authors thank Federico Monzon, MD for his expert advice and intellectual guidance while writing and revising this manuscript, as well as Alison Fitzgerald, PhD for her intellectual contributions (both employees at Castle Biosciences, Inc.).