Microarray analysis of lncRNA and mRNA expression profiles in sinonasal inverted papilloma
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ABSTRACT:
PROVIDER: PRJNA794137 | ENA |
REPOSITORIES: ENA
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Project description:To explore the expression profile, potential functions, and diagnostic and clinicopathological significance of lncRNAs in sinonasal inverted papilloma (SNIP).The expression profiles of lncRNAs and mRNAs were analyzed using a microarray. The potential functions and clinical implications of specific lncRNAs were further analyzed by bioinformatics and statistical methods.
2022-01-05 | GSE193016 | GEO
Project description:OBJECTIVE: Although the malignant transformation of sinonasal inverted papilloma (SNIP) into squamous cell carcinomas (SCC) has been reported in the literature, the molecular mechanisms driving this transformation have not been elucidated. This study compares genome-wide DNA methylation between SNIP and SCC arising in SNIP and further validates the expression of aberrantly methylated genes. Methots:We used a comprehensive methylation profiling technique to investigate DNA methylation in CpG islands and promoters in six SNIP samples and seven SCC arising in SNIP samples. A total of 11,201 nominally differentially methylated sites were observed, between SNIP and SCC arising in SNIP. This study is the first to compare the differences in global DNA methylation between SNIP and SCC arising in SNIP.
2019-01-22 | GSE125399 | GEO
Project description:Putative Biomarkers of malignant transformation of sinonasal inverted papilloma into squamous cell carcinoma
| PRJNA516218 | ENA
Project description:Long non-coding RNAs (lncRNAs) play important roles in various biological progresses of carcinogenesis. However, the function of lncRNAs in human sinonasal squamous cell carcinoma (SNSCC) remains greatly unclear. In the current study, lncRNA AC091729.7 expression was examined in SNSCC samples by using microarray.The human 8 × 60 K lncRNA array was produced by Arraystar Company (USA). Over 25,000 lncRNAs were gathered from the canonical data sources encompassing UCSC, NCBI RefSeq, RNAdb, and NRED.
2019-10-15 | GSE138809 | GEO
Project description:LncRNA Expression Profiling in sinonasal squamous cell carcinomas
| PRJNA577404 | ENA
Project description:Inverted sinonasal papilloma (ISP) is a locally aggressive neoplasm associated with sinonasal squamous cell carcinoma (SNSCC) in 10% to 25% of cases. To date, no recurrent mutations have been identified in ISP or SNSCC. Using targeted next-generation sequencing and Sanger sequencing, we identified activating EGFR mutations in 88% of ISP and 77% of ISP-associated SNSCC. Identical EGFR genotypes were found in matched pairs of ISP and associated SNSCC, providing the first genetic evidence of a biologic link between these tumors. EGFR mutations were not identified in exophytic or oncocytic papillomas or non-ISP-associated SNSCC, suggesting that the ISP/SNSCC spectrum is biologically distinct among sinonasal squamous tumors. Patients with ISP harboring EGFR mutations also exhibited an increased progression-free survival compared with those with wild-type EGFR. Finally, treatment of ISP-associated carcinoma cells with irreversible EGFR inhibitors resulted in inactivation of EGFR signaling and growth inhibition. These findings implicate a prominent role for activating EGFR mutations in the pathogenesis of ISP and associated SNSCC and rationalize consideration of irreversible EGFR inhibitors in the therapy of these tumors.
| S-EPMC4508878 | biostudies-literature
Project description:Objective We review our institution's experience with the treatment of inverted papilloma (IP) with emphasis on the implications of surgical margins for disease control. Design Retrospective chart review of patients with IP treated at the University of Michigan from 1996 to 2011. Setting Tertiary care center. Participants Patients undergoing surgical resection with curative intent for IP. Main Outcome Measures Overall survival, disease-specific survival, and locoregional control were used as main outcome measures. Results We studied 129 patients including 19 with carcinoma arising from IP. Disease-free rates at 2, 3, and 5 years were 79.7%, 77.9%, and 61%, respectively. Overall, 10 of 18 recurrences were detected > 2 years from follow-up, with recurrences detected up to 8 years from surgery. For benign disease, obtaining tissue margins outside of the primary specimen for margin control did not affect disease control rates. Conclusion IP is a disease that requires significant follow-up periods beyond 2 years. For IP without carcinogenesis, acquiring margins outside of the tumor specimen did not appear to affect disease control rates in this study. No clear predictors of malignancy were seen in this study, which highlights the need for further research to predict this phenomenon.
| S-EPMC3969439 | biostudies-other
Project description:PurposeAccurate preoperative prediction of the malignant transformation of sinonasal inverted papilloma (IP) is essential for guiding biopsy, planning appropriate surgery and prognosis of patients. We aimed to investigate the value of MRI-based radiomics in discriminating IP from IP-transformed squamous cell carcinomas (IP-SCC).MethodsA total of 236 patients with IP-SCC (n=92) or IP (n=144) were enrolled and divided into a training cohort and a testing cohort. Preoperative MR images including T1-weighted, T2-weighted, and contrast enhanced T1-weighted images were collected. Radiomic features were extracted from MR images and key features were merged into a radiomic model. A morphological features model was developed based on MR morphological features assessed by radiologists. A combined model combining radiomic features and morphological features was generated using multivariable logistic regression. For comparison, two head and neck radiologists were independently invited to distinguish IP-SCC from IP. The area under the receiver operating characteristics curve (AUC) was used to assess the performance of all models.ResultsA total of 3948 radiomic features were extracted from three MR sequences. After feature selection, we saved 15 key features for modeling. The AUC, sensitivity, specificity, and accuracy on the testing cohort of the combined model based on radiomic and morphological features were respectively 0.962, 0.828, 0.94, and 0.899. The diagnostic ability of the combined model outperformed the morphological features model and also outperformed the two head and neck radiologists.ConclusionsA combined model based on MR radiomic and morphological features could serve as a potential tool to accurately predict IP-SCC, which might improve patient counseling and make more precise treatment planning.
| S-EPMC8983836 | biostudies-literature
Project description:ObjectiveTo investigate the diagnostic performance of quantitative and semi-quantitative parameters derived from dynamic contrast-enhanced MRI (DCE-MRI) in differentiating sinonasal inverted papilloma (SIP) from SIP with coexisting malignant transformation into squamous cell carcinoma (MT-SIP).MethodsThis retrospective study included 122 patients with 88 SIP and 34 MT-SIP. Quantitative and semi-quantitative parameters derived from DCE-MRI were compared between SIP and MT-SIP. The multivariate logistic regression analysis was performed to identify independent indicators and construct regression model for distinguishing MT-SIP and SIP. Diagnostic performance of independent indicators and regression model were evaluated using receiver operating coefficient (ROC) analysis and compared using DeLong test.ResultsThere were significant differences in maximum slope of increase, contrast-enhancement ratio, bolus arrival time, volume of extravascular extracellular space (Ve), and rate constant (Kep) between SIP and MT-SIP (p < 0.05). There were no significant differences in initial area under the gadolinium curve (p = 0.174) and volume transfer constant (p = 0.105) between two groups. Multivariate analysis results showed that Ve and Kep were identified as the independent indicators for differentiating MT-SIP from SIP (p < 0.001). Areas under the ROC curves (AUCs) for predicting MT-SIP were 0.779 for Ve and 0.766 for Kep. The AUC of the combination of Ve and Kep was 0.831, yielding 83% specificity and 76.5% sensitivity.ConclusionDCE-MRI can quantitatively differentiate between MT-SIP and SIP. The combination of Ve and Kep yielded an optimal performance for discriminating SIP from its malignant mimics.Advances in knowledgeDCE-MRI with quantitative and semi-quantitative parameters can provide valuable evidences for quantitatively identifying MT-SIP.
| S-EPMC10996421 | biostudies-literature
Project description:Recently, the specific association between Sinonasal inverted papilloma (SIP) and EGFR exon 20 mutations has been reported. To investigate the link between specific EGFR mutations and SIP development, we established organotypic raft culture system using nasal polyp-derived immortalized NP2 (iNP2) cells expressing EGFR exon 20 mutants or an exon 19 mutant, and SIP-derived iIP4 cells harboring P772_H773insPYNP mutation. In the raft culture, iIP4 cells showed the inverted growth pattern characteristic to SIP. Interestingly, iNP2 cells expressing EGFR exon 20 duplication mutants, S768_D770dup and N771_H773dup, but not of EGFR exon 19 mutant, E746_A750del, showed the inverted growth pattern. Enhanced activation of the PI3K/AKT signaling pathway was observed in iNP2_S768_D770dup and iIP4 cells, while increased MAPK signaling was found in iNP2_N771_H773dup. Increased cell migration and invasion were found in all cells carrying EGFR mutations when compared to iNP2 cells, and this effect was inhibited by either PI3K or MEK inhibitor. Notably, iNP2 cells expressing the N771_H773dup mutant showed the highest migration and invasion abilities. These results suggest that specific mutations in EGFR exon 20 play a crucial role in SIP development, partially though hyper-activation of the PI3K/AKT and MAPK signaling pathways. This study presents the first in vitro model for SIP development, which could facilitate further investigations into SIP pathogenesis and preclinical studies for new therapeutic agents.
| S-EPMC10611779 | biostudies-literature