A Four-Gene Signature Model Improves the Prediction of Distant Metastasis in Patients with Nasopharyngeal Carcinoma: A Retrospective, Three-Center Observational Study

Background: Similar to that in other malignant tumors, distant metastasis is one of the most important causes of poor prognosis in nasopharyngeal carcinoma (NPC). However, the genetic hallmarks and networks that regulate the distant metastasis of NPC are not fully understood. Methods: In this study, we performed high-throughput screening of mRNA expression profiles in 92 NPC samples collected from 3hospitals and detected the mRNA expression levels of 31,503 genes in these samples. Gene functional enrichment analyses were performed using gene set enrichment analysis (GSEA). Least absolute shrinkage and selection operator (LASSO) was applied to select prognostic genes and a Cox proportional hazards regression model including these genes was constructed to predict prognosis. The Kaplan-Meier curve and time-dependent receiver operating characteristic (ROC) curve were plotted to assess the performance of this model. Univariate and multivariate analyses were performed using the Cox proportion hazard model to test the independence of prognostic effect of gene model and other clinical features. Results: A total of 1837 differentially expressed genes between patients with and without distant metastasis were identified in the training cohort, including 869 upregulated genes and 968 downregulated genes. Six gene sets, including the Wnt/β catenin signaling pathway, hedgehog (Hh) signaling pathway, Notch signaling pathway, mitotic spindle, apical surface, and estrogen response late, were enriched in patients with distant metastasis. A four-gene signature model was constructed in the training cohort, and according to the time-dependent ROC curve, this model had certain accuracy in predicting distant metastasis-free survival (DMFS) in both the training and validation cohorts. Conclusion: We developed a four-gene signature model that can evaluate the distant metastasis risk of NPC patients and may also provide novel therapeutic targets for NPC treatment in the near future.

Long non-coding RNA CRNDE exacerbates NPC advancement mediated by the miR-545-5p/CCND2 axis

BACKGROUND

Previous studies indicated CRNDE to have a pivotal part within tumorigenesis. Notwithstanding, precise details on CRNDE activities within NPC are still uncertain. The investigation described in this article served to focus in greater depth on the mechanistics regarding CRNDE, together with all associated regulatory networks, on nasopharyngeal carcinoma (NPC) and its treatment possibilities.

METHODS

Quantitative real-time polymerase chain reaction (RT-qPCR) analyzed CRNDE, miR-545-5p and CCND2 expression within NPCs and representative cell lineages. CCK-8 cell counting-, EdU-, wound-healing-/transwell-assays analyzed cellular proliferation, migrative, together with invasive properties. Apoptosis/cell cycle progression were scrutinized through flow cytometry. Dual-luciferase reporter assays validated CRNDE/miR-545-5p/CCND2 interplay. Proteomic expression of apoptosis-related protein, EMT-related protein and CCND2 protein were evaluated through Western blotting. In addition, Ki67 expression was evaluated through immunohistochemical staining. The effect of CRNDE in vivo was assessed by nude murine xenograft model studies.

RESULTS

This study demonstrated up-regulated expression of CRNDE and CCND2 within NPC tissues/cell lines. Meanwhile, miR-545-5p was down-regulated. CRNDE knock-down or miR-545-5p over-expression drastically reduced NPC proliferative, migrative and invasive properties, promoted apoptosis/altered cell cycle, and inhibited CCND2 expression. However, miR-545-5p down-regulation had opposing effects. All inhibiting functions generated by CRNDE down-regulation upon NPC progression could be counterbalanced or synergistically exacerbated, depending on miR-545-5p down-regulation or up-regulation, respectively. Multiple-level investigations revealed CRNDE to serve as a sponge for miR-545-5p, and can target CCND2 within NPCs.

CONCLUSIONS

CRNDE increases CCND2 expression by competitive binding with miR-545-5p, thus accelerating the development of NPC. This provides potential therapeutic targets and prognostic markers against NPC.

Phase II study of induction chemotherapy followed by concurrent chemoradiotherapy with raltitrexed and cisplatin in locally advanced nasopharyngeal carcinoma

Objective

For locally advanced nasopharyngeal carcinoma (LA-NPC) patients, high incidences of distant metastases and severe treatment related toxicities are the main obstacles needed to be overcome. Raltitrexed, a specific thymidylate synthase inhibitor with a convenient administration schedule, has an acceptable and manageable toxicity, and possesses radio-sensitizing properties. To investigate the efficacy and safety of raltitrexed and cisplatin induction chemotherapy and concurrent chemoradiotherapy (IC+CCRT) in patients with LA-NPC, a phase II clinical study was conducted.

Methods

Sixty eligible patients with LA-NPC were enrolled into this study. A raltitrexed-cisplatin combination was used as part of an IC+CCRT regimen. Raltitrexed-cisplatin IC was given once every 3 weeks (q3w) for two cycles, followed by raltitrexed-cisplatin based CCRT q3w for two cycles. Intensity-modulated radiotherapy (IMRT) was given for all enrolled patients.

Results

All patients were included in survival analysis according to the intent-to-treat principle. The objective response rate (ORR) 3 months after treatment was 98%. The 2-year overall survival (OS) rate was 92%. The median relapse-free survival (RFS) time was 30.5 [95% confidence interval (95% CI), 28.4−32.3] months. The 2-year RFS rate was 85%. The 2-year local failure-free survival (LFFS) rate was 97% and the 2-year distant metastasis-free survival (DMFS) rate was 88%. Acute toxicities were mostly grade 2 and 3 reactions in bone marrow suppression, gastrointestinal side effect and oropharyngeal mucositis. Only two patients occurred grade 4 acute toxicities, one was bone marrow suppression and the other was dermatitis radiation.

Conclusions

The combination of raltitrexed and cisplatin has a comparable efficacy to those in standard first-line therapy.

MRI-Based Deep-Learning Model for Distant Metastasis-Free Survival in Locoregionally Advanced Nasopharyngeal Carcinoma

BACKGROUND

Distant metastasis is the primary cause of treatment failure in locoregionally advanced nasopharyngeal carcinoma (LANPC).

PURPOSE

To develop a model to evaluate distant metastasis-free survival (DMFS) in LANPC and to explore the value of additional chemotherapy to concurrent chemoradiotherapy (CCRT) for different risk groups.

STUDY TYPE

Retrospective.

POPULATION

In all, 233 patients with biopsy-confirmed nasopharyngeal carcinoma (NPC) from two hospitals.

FIELD STRENGTH

1.5T and 3T.

SEQUENCE

Axial T₂ -weighted (T₂ -w) and contrast-enhanced T₁ -weighted (CET₁ -w) images.

ASSESSMENT

Deep learning was used to build a model based on MRI images (including axial T₂ -w and CET₁ -w images) and clinical variables. Hospital 1 patients were randomly divided into training (n = 169) and validation (n = 19) cohorts; Hospital 2 patients were assigned to a testing cohort (n = 45). LANPC patients were divided into low- and high-risk groups according to their DMFS (P < 0.05). Kaplan-Meier survival analysis was performed to compare the DMFS of different risk groups and subgroup analysis was performed to compare patients treated with CCRT alone and treated with additional chemotherapy to CCRT in different risk groups, respectively.

STATISTICAL TESTS

Univariate analysis was performed to identify significant clinical variables. The area under the receiver operating characteristic (ROC) curve (AUC) was used to assess the model performance.

RESULTS

Our deep-learning model integrating the deep-learning signature, node (N) stage (from TNM staging), plasma Epstein-Barr virus (EBV)-DNA, and treatment regimens yielded an AUC of 0.796 (95% confidence interval [CI]: 0.729-0.863), 0.795 (95% CI: 0.540-1.000), and 0.808 (95% CI: 0.654-0.962) in the training, internal validation, and external testing cohorts, respectively. Low-risk patients treated with CCRT alone had longer DMFS than patients treated with additional chemotherapy to CCRT (P < 0.05).

DATA CONCLUSION

The proposed deep-learning model, based on MRI features and clinical variates, facilitated the prediction of DMFS in LANPC patients.

LEVEL OF EVIDENCE

3.

TECHNICAL EFFICACY STAGE

4.

A Gene-Expression Predictor for Efficacy of Induction Chemotherapy in Locoregionally Advanced Nasopharyngeal Carcinoma

BACKGROUND

Induction chemotherapy (IC) followed by concurrent chemoradiotherapy is the mainstay treatment for patients with locoregionally advanced nasopharyngeal carcinoma. However, some patients obtain little benefit and experience unnecessary toxicities from IC. We intended to develop a gene-expression signature that can identify beneficiaries of IC.

METHODS

We screened chemosensitivity-related genes by comparing gene-expression profiles of patients with short-term tumor response or nonresponse to IC (n = 95) using microarray analysis. Chemosensitivity-related genes were quantified by digital expression profiling in a training cohort (n = 342) to obtain a gene signature. We then validated this gene signature in the clinical trial cohort (n = 187) and an external independent cohort (n = 240). Tests of statistical significance are 2-sided.

RESULTS

We identified 43 chemosensitivity-related genes associated with the short-term tumor response to IC. In the training cohort, a 6-gene signature was developed that was highly accurate at predicting the short-term tumor response to IC (area under the curve [AUC] = 0.87, sensitivity = 87.5%, specificity = 75.6%). We further found that IC conferred failure-free survival benefits only in patients in the benefit group (hazard ratio [HR] = 0.54, 95% confidence interval [CI] = 0.34 to 0.87; P = .01) and not on those in the no-benefit group (HR = 1.25, 95% CI = 0.62 to 2.51; P = .53). In the clinical trial cohort, the 6-gene signature was also highly accurate at predicting the tumor response (AUC = 0.82, sensitivity = 87.5%, specificity = 71.8%) and indicated failure-free survival benefits. In the external independent cohort, similar results were observed.

CONCLUSIONS

The 6-gene signature can help select beneficiaries of IC and lay a foundation for a more individualized therapeutic strategy for locoregionally advanced nasopharyngeal carcinoma patients.

Overexpression of the 14-3-3γ protein in uterine leiomyoma cells results in growth retardation and increased apoptosis

Protein 14-3-3γ was significantly reduced in human uterine leiomyoma compared to the adjacent normal myometrium tissue. To investigate the possible link between the reduced 14-3-3γ expression and uterine leiomyoma growth, we have overexpressed 14-3-3γ protein in uterine leiomyomal cells and its effects on cell proliferation and apoptosis were analyzed. Over-expression of 14-3-3γ was achieved by transducing into two types of uterine leiomyoma cells (primary culture cells and immortal stem cells) with a 14-3-3γ expressing adenovirus vector. Differentially expressed proteins were screened by the proteomics tool (TMT-LCTMS), followed by PANTHER database analysis to single out specifically modified signaling pathway proteins, which were confirmed by Phospho-MAPK Antibody Array and Western blots analysis. The results showed that increase in 14-3-3γ expression in both two types of human uterine leiomyoma cells inhibited cell proliferation and induced apoptosis. Proteomic screening has found 42 proteins, among 5846, that were significantly affected. PANTHER database and GeneMANIA analysis of the differentially expressed proteins have found that proteins involved in apoptosis signaling and cytoskeletal/adhesion were among the ones affected the most. Further analysis of the key signaling pathways have found that over-expression of 14-3-3γ resulted in reductions in the phosphorylations of multiple signaling molecules, including AKT, pan, ERK1/2, GSK-3 α/β, MEK1/2, Foxo1 and Vimentin. In conclusion, the loss of 14-3-3γ may have causal effects on the growth of uterine leiomyoma, which may function through modifying multiple signaling pathways, including AKT-Foxo and/or MEK1/2-ERK1/2.

The Effects of Guizhi Fuling Capsule Drug Serum on Uterine Leiomyoma Cells and Its Mechanism

Aims. To observe the effects of Guizhi Fuling Capsule (GZFLC) drug serum on uterine leiomyoma cells and explore its mechanism. Main Methods. Sixty Sprague Dawley rats were randomly divided into two groups (normal saline lavage group and GZFLC lavage group), then, respectively, blank serum and GZFLC drug serum were collected, and finally human uterine leiomyoma cells were treated. Human leiomyoma tissues were collected from 20 patients who underwent uterine leiomyomas operations, and leiomyoma cells were primary cultured. The leiomyoma cells were treated by GZFLC drug serum in different concentrations (10%, 20%, and 30%) and variable treatment time (12 h, 24 h, 36 h, 48 h, and 72 h). Cell proliferation was observed using CCK8 assay. Flow cytometry and Annexin V/PI were used to assay the effects of GZFLC drug serum on cell apoptosis. Western blot analysis was used to assay the effects of GZFLC drug serum on TSC2, FOXO, and 14-3-3γ expression in uterine leiomyoma cells. Key Findings. In the concentrations of 10%～30%, GZFLC drug serum could inhibit proliferation of leiomyoma cells in dose-dependent manner; at the time of 36 h, cell inhibition rate was at the peak; GZFLC drug serum could induce apoptosis of leiomyoma also in a dose-dependent manner, and apoptosis rate quickly achieved maximum at 12 h time points, and then second apoptosis peak appeared at 36 h. Compared to nontreatment group, TSC2, FOXO, and 14-3-3γ expressions in drug serum group were significantly changed after 12 h treatment. Significance. GZFLC drug serum can efficiently inhibit the proliferation and induce apoptosis of leiomyoma cells, which is related to the 14-3-3γ pathway.

Omics-based identification of biomarkers for nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a head and neck cancer that is highly found in distinct geographic areas, such as Southeast Asia. The management of NPC remains burdensome as the prognosis is poor due to the late presentation of the disease and the complex nature of NPC pathogenesis. Therefore, it is necessary to find effective molecular markers for early detection and therapeutic measure of NPC. In this paper, the discovery of molecular biomarker for NPC through the emerging omics technologies including genomics, miRNA-omics, transcriptomics, proteomics, and metabolomics will be extensively reviewed. These markers have been shown to play roles in various cellular pathways in NPC progression. The knowledge on their function will help us understand in more detail the complexity in tumor biology, leading to the better strategies for early detection, outcome prediction, detection of disease recurrence, and therapeutic approach.

Identification of module biomarkers from the dysregulated ceRNA–ceRNA interaction network in lung adenocarcinoma

The dysregulated ceRNA–ceRNA interaction network in lung adenocarcinoma.

Quantitative proteome analysis of overexpressed Cripto-1 tumor cell reveals 14-3-3γ as a novel biomarker in nasopharyngeal carcinoma

We previously found that Cripto-1 is involved in the tumorigenesis of nasopharyngeal carcinoma (NPC). Here, to identify new NPC related proteins and to investigate the clinicopathological correlations of it in NPC, Cripto-1 over-expressed cell (CNE1/CR1(+)) was established. Two-dimensional difference in gel electrophoresis (2D-DIGE) analysis and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) were used to identify 23 differential proteins in CNE1/CR1(+) and parental cells. Among them, 14-3-3γ showed the potential to be a NPC related protein. 14-3-3γ expression was found in 58.3% (60/103) tumor tissues as detected by IHC, and 69.6% (16/23) NPC fresh tumors expressed higher 14-3-3γ than paired non-cancerous tissues as detected by Western blot. Moreover, 14-3-3γ expression was positively correlated with N classification (p=0.031), distant metastasis (M classification, p=0.018) and clinical stage (p=0.046) of NPC patients. As determined by the Kaplan-Meier method, 14-3-3γ expression in NPC was significantly associated with overall survival (p=0.015). Multivariate analysis also showed that the expression of 14-3-3γ protein was an independent prognostic factor for outcome of NPC. In this study, we identified upregulated 14-3-3γ by 2D-DIGE in CNE1/CR-1(+). We also demonstrated that 14-3-3γ might be a potential biomarker for the prognosis of patients with NPC.

BIOLOGICAL SIGNIFICANCE

We believe that three aspects of this manuscript will make it interesting to general readers of Journal of Proteomics. Firstly, based on our previous report, we further validated that Cripto-1 can promote the proliferation and invasion of nasopharyngeal carcinoma (NPC). In this context, we used 2D-DIGE to identify new NPC related proteins. As a result, 14-3-3γ showed the potential to be a candidate. Secondly, we reported for the first time that the expression level of 14-3-3γ was significantly increased in human NPC patient tissues, and 14-3-3γ overexpression correlated statistically with N classification, distant metastasis, and clinical stage. Our results highlight the clinical significance of 14-3-3γ in NPC. Finally, we found that high 14-3-3γ expression is associated with poor survival in NPC patients. Thus, this study has identified that the 14-3-3γ involves in the carcinogenesis of NPC. Our findings may also provide new insights into understanding the molecular mechanism involved in NPC carcinogenesis and progression, and may lead to the development of new approaches for effective diagnosis and therapy.

Proteomic features of potential tumor suppressor NESG1 in nasopharyngeal carcinoma

We previously defined the recently revised NESG1 gene as a potential tumor suppressor in nasopharyngeal carcinoma (NPC). Here, we further used proteomics technology to globally examine NESG1-controlled proteins in NPC cells. Twenty-six proteins were found to be deregulated by NESG1 using proteomics analysis while enolase 1 (alpha) (ENO1), heat shock protein 90 kDa beta (Grp94), member 1 (HSP90B1), and cathepsin D (CTSD) proteins were differentially expressed by Western blot. Interestingly, a-enolase (ENO1), an overexpressed gene in NPC, was confirmed as a NESG1-regulated protein in NPC cells. Overexpressed ENO1 not only restored cell proliferation and cell-cycle progression, but also antagonized the regulation of NESG1 to cell-cycle regulators p21 and CCNA1 expression as well as induced the expression of C-Myc, pRB, and E2F1 in NESG1-ovexpressed NPC cells. Real-time PCR and immunohistochemistry analysis showed that NESG1 expression is negatively correlated with ENO1 expression in NPC tissues. Our observations suggest that ENO1 downregulation plays an important role in NESG1-induced growth inhibition of NPC cancer cells.

Integrated analysis of multiple gene expression profiling datasets revealed novel gene signatures and molecular markers in nasopharyngeal carcinoma

PURPOSE

To identify the novel gene signatures and molecular markers of nasopharyngeal carcinoma (NPC) by integrated bioinformatics analysis of multiple gene expression profiling datasets.

EXPERIMENTAL DESIGN

Seven published gene expression profiling studies and one of our unpublished works were reanalyzed to identify the common significantly dysregulated (CSD) genes in NPC. Overrepresentation analysis of cytogenetic bands, Gene Ontology (GO) categories, pathways were used to explore CSD genes functionally associated with carcinogenesis. The protein expressions of selected CSD genes were examined by immunohistochemistry on tissue microarrays, and the correlations of their expressions with clinical outcomes were evaluated.

RESULTS

Using the criteria (genes reported deregulated in more than one study), a total of 962 genes were identified as the CSD genes in NPC. Four upregulated (BUB1B, CCND2, CENPF, and MAD2L1) and two downregulated (LTF and SLPI) genes were markedly reported in six studies. The enrichments of chromosome aberrations were 2q23, 2q31, 7p15, 12q15, 12q22, 18q11, and 18q12 in upregulated genes and 14q32 and 16q13 in downregulated genes. The activated GO categories and pathways related to proliferation, adhesion, invasion, and downregulated immune response had been functionally associated with NPC. SLPI significantly downregulated in nasopharyngeal adenocarcinoma. Furthermore, the high expression of BUB1B or CENPF was associated with poor overall survival of patients.

CONCLUSION

It was first clearly identified the dysregulated expression of BUB1B and SLPI in NPC tissues.

IMPACT

Further studies of the CSD genes as gene signatures and molecular markers of NPC might improve the understanding of the disease and identify new therapeutic targets.