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Background  The aim of this study was to elucidate the value of putative cancer stem cell markers Musashi-1, ALDH1, Sox2, and CD49f in predicting the prognosis in cervical squamous cell carcinoma (CSCC).    Methods  Real-time PCR and immunohistochemistry staining was performed to examine Musashi-1, ALDH1, Sox2, and CD49f expression in archived specimens of CSCC patients with postoperative chemotherapy. Kaplan–Meier analysis and Cox proportional hazards model were used to assess the prognostic impact of CSC markers for overall survival (OS) and recurrent-free survival (RFS).    Results  The Real-time PCR data showed that the expression of all markers were increased in CSCC tissues compared with in paired normal cervical tissues ( P  < 0.05). The IHC result showed that high expression of Msi1, ALDH1, Sox2, and CD49f was found in 25.7 %, 43.0 %, 62.0 % and 29.0 % CSCC samples, respectively. Moreover, high expression of Msi1 ( P  = 0.033 and  P  = 0.003, respectively), ALDH1 ( P  = 0.015 and  P  = 0.002, respectively), and Sox2 ( P  = 0.005 and  P  = 0.003, respectively), and low expression of CD49f ( P  = 0.027 and  P  = 0.025, respectively) were correlated with poor OS and PFS in CSCC patients. Interestingly, tumors with Msi1 high /CD49f low  expression had the poorest prognosis according to Msi1/CD49f stratification. In multivariate Cox regression analysis, Sox2 expression ( P  = 0.047 and  P  = 0.018, respectively), ALDH1 expression ( P  = 0.013 and  P  = 0.003, respectively), and CD49f expression ( P  = 0.008 and  P  = 0.003, respectively) were independent prognostic markers for both OS and RFS.    Conclusions  Our results suggest that cancer stem cell markers are linked with poor prognosis of CSCC patients.    Electronic supplementary material  The online version of this article (doi:10.1186/s12885-015-1826-4) contains supplementary material, which is available to authorized users.

Putative stem cell markers in cervical squamous cell carcinoma are correlated with poor clinical outcome