In this study, we have demonstrated that the malignancy-risk gene signature is a prognostic and predictive indicator in early-stage NSCLC. In our previous study (27
), the signature was shown to be capable of discriminating molecularly abnormal breast tissues that appear histologically normal from molecularly normal breast tissues. Both observations suggest that expression of genes in the malignancy-risk gene signature may contribute to carcinogenesis in lung and breast cancer (35
). The malignancy-risk gene signature was derived from a comparison of normal breast tissue with invasive ductal carcinomas (27
). A majority of the genes in the malignancy-risk signature are core regulators of the mammalian cell cycle and are essential for DNA replication and repair (38
). The application of the malignancy-risk gene signature to both breast and lung cancers may not be surprising because sustained proliferative signaling has been considered one of the earliest and most fundamental hallmarks of cancer cells for the past decade (39
Several gene signatures have been developed to predict outcome in NSCLC (14
). Generally these gene signatures are not composed of genes involved in proliferation and few malignancy-risk genes overlapped with these signatures. In fact, a common biology underlying these previously defined gene signatures has not been described. Nonetheless, our study showed that the malignancy-risk gene signature, a proliferative gene signature, is associated with both cancer risk and progression. One might predict that a gene signature derived from the Director’s Challenge Consortium dataset of lung cancers could have better prognostic and predictive value than the malignancy-risk gene signature because there may be substantial differences between lung and breast cancer, and the gene signature derived from the breast tissue may not be optimal for lung cancer. Surprisingly, a gene signature derived on the basis of high correlation with OS in the Director’s Challenge Consortium dataset was prognostic but not predictive (data not shown). Furthermore, majority of genes in the malignancy-risk signature were absent in this signature, as has been reported for other gene signatures (20
) derived from this database. Why these strongly prognostic and predictive genes do not appear in these analyses is unclear. What is clear is that different approaches may lead to different gene signatures.
There are a few gene signatures developed in breast cancer and tested in lung cancer, although they do not completely overlap with the malignancy-risk gene signature and are either a metastasis signature (26
) or a prognostic signature (24
). In contrast, the malignancy-risk gene signature features both prognostic and predictive factors in NSCLC and shares some unique clinical features in both lung and breast cancer. The expression of the majority of malignancy-risk genes was increased in breast cancer and also was associated with poorer survival in lung cancer. In addition, a strong correlation of the loading coefficients was reported between the two tumor types. To our best knowledge, our study is the first to show such a high consistency of the gene signature in both tumor types. The malignancy-risk gene signature showed clinical association with cancer relapse/progression, and prognosis in the breast cancer (41
). Similarly, the gene signature demonstrated a statistically significant association with OS and other clinical predictors in NSCLC (TNM stage and histological grade). Collectively, these findings suggest transferability of the malignancy-risk gene signature between breast and lung cancer, one unique feature not seen in other gene signatures derived for various tumor types (24
From the predictive aspect, the malignancy-risk gene signature has demonstrated the potential to identify early-stage NSCLC patients likely to benefit from ACT. A 15-gene signature described by Zhu et al. (29
) was the first predictive signature for ACT in resected NSCLC, derived from the randomized phase III JBR.10 trial (8
). However, the malignancy-risk gene signature also showed a statistically significant predictive value comparable with that on the reverse transcription polymerase chain reaction basis reported by Zhu et al. (29
) with no overlap between the genes in both signatures. This observation suggests that the relationship between a survival benefit and ACT could be also affected expression of the genes included in the malignancy-risk gene signature. Specifically, the survival benefit from ACT relative to the observation cohort was considerably greater in the high malignancy-risk group. In contrast, the survival benefit of ACT vs the observation cohort was not statistically significant in the low malignancy-risk group; however, the observation cohort seemed to have the advantage in OS for the first 2 years compared with those receiving ACT. In addition, evaluation of the predictive value in the Director’s Challenge Consortium dataset indirectly supported the utility of the signature, although it was a retrospective study. Together, these results suggest that the malignancy-risk gene signature is a strong predictive factor for a differential OS benefit from ACT. Although recent multinational clinical trials (4
) have established that ACT is associated with improvement of OS in patients with early-stage NSCLC, the malignancy-risk gene signature may provide an additional tool to help identify a subset patients at high-risk of death who may benefit from ACT.
Similar to other prognostic signatures (15
), the malignancy-risk gene signature was able to predict OS in NSCLC patients. Patients with a high malignancy-risk score tended to have shorter OS compared with those who had a low malignancy-risk score. In addition, subgroup analysis showed the malignancy-risk signature’s value beyond the conventional clinical predictors with a statistically significant association of the gene signature with OS in one or more risk groups for each clinical predictor. In particular, the malignancy-risk gene signature was able to consistently distinguish between the two risk groups (low and high malignancy-risk groups, respectively, corresponding to good and poor OS) in the subgroups of stage IB patients and stage IB patients who had a history of smoking. Because the benefit of ACT remains unclear in stage IB NSCLC (4
), the signature may have potential clinical application for stage IB patients, such as recommendation of ACT only for stage IB patients with a high malignancy-risk score. The utility of the signature for treatment management in stage IB still needs to be further evaluated in a prospective ACT clinical trial.
Our study has some limitations. We have shown the prognostic and predictive values of the malignancy-risk gene signature using three publicly available NSCLC microarray datasets. However, to be considered as a personalized medicine strategy for clinical decision making, validation of the malignancy-risk gene signature in an independent dataset, larger or at least comparable with the Director’s Challenging Consortium dataset, is needed. Successful validation will advance the malignancy-risk gene signature to the next level for the analytical and clinical validity. We plan to evaluate the malignancy-risk gene signature and complete a large-scale validation using microarray data from Total Cancer Care (42
) collected at the Moffitt Cancer Center. Second, the microarray datasets in our study used fresh frozen tissues to extract RNA to measure gene expression. Although fresh frozen tissues are commonly used in research communities for microarray experiments, formalin-fixed and paraffin-embedded tissues are often collected in community-based hospitals. If the malignancy-risk gene signature could be validated in formalin-fixed and paraffin-embedded tissues, the signature would be a great clinical utility for broad application in personalizing treatment care. A recent study has demonstrated the feasibility of using formalin-fixed and paraffin-embedded tissues for gene signature development in NSCLC (22
In summary, the malignancy-risk gene signature could be useful to improve prediction of OS in NSCLC patients and is a potential tool to more accurately identify patients who will benefit from adjuvant therapy after surgical resection. Future prospective studies are needed to determine if the malignancy-risk score can be used clinically to benefit early-stage NSCLC patients.