Stages Of Epithelial Cell Differentiation Research Articles

Integrative Analysis of miRNAs Identifies Clinically Relevant Epithelial and Stromal Subtypes of Head and Neck Squamous Cell Carcinoma

The objective of this study is to characterize the role of miRNAs in the classification of head and neck squamous cell carcinoma (HNSCC). Here, we analyzed 562 HNSCC samples, 88 from a novel cohort and 474 from The Cancer Genome Atlas, using miRNA microarray and miRNA sequencing, respectively. Using an integrative correlations method followed by miRNA expression-based hierarchical clustering, we validated miRNA clusters across cohorts. Evaluation of clusters by logistic regression and gene ontology approaches revealed subtype-based clinical and biological characteristics. We identified two independently validated and statistically significant (P < 0.01) tumor subtypes and named them "epithelial" and "stromal" based on associations with functional target gene ontology relating to differing stages of epithelial cell differentiation. miRNA-based subtypes were correlated with individual gene expression targets based on miRNA seed sequences, as well as with miRNA families and clusters including the miR-17 and miR-200 families. These correlated genes defined pathways relevant to normal squamous cell function and pathophysiology. miRNA clusters statistically associated with differential mutation patterns including higher proportions of TP53 mutations in the stromal class and higher NSD1 and HRAS mutation frequencies in the epithelial class. miRNA classes correlated with previously reported gene expression subtypes, clinical characteristics, and clinical outcomes in a multivariate Cox proportional hazards model with stromal patients demonstrating worse prognoses (HR, 1.5646; P = 0.006). We report a reproducible classification of HNSCC based on miRNA that associates with known pathologically altered pathways and mutations of squamous tumors and is clinically relevant.

Abstract 5448: Integrative analysis of microRNA expression identifies two biologically distinct and clinically relevant subtypes of head and neck squamous cell carcinoma

Abstract Purpose: The objective of this study is to investigate the potential role of microRNAs (miRNA) as molecular markers of tumor heterogeneity in head and neck squamous cell carcinoma (HNSCC). Experimental Design: Here, we analyzed 562 HNSCC samples, 88 from a novel cohort and 474 from The Cancer Genome Atlas (TCGA), using miRNA-microarray and miRNA-seq, respectively. Using an integrative correlations method followed by miRNA expression-based hierarchical clustering, we validated miRNA clusters across cohorts, and evaluation of clusters by logistic regression and gene ontology approaches revealed subtype-based clinical and biological characteristics. Results: We identified two statistically significant tumor subtypes and named them ‘epithelial' and ‘stromal' based on correlations with functional target gene ontology in relation to differing stages of epithelial cell differentiation. Each subtype demonstrated significant differences in terms of mRNA signature (p &amp;lt; 0.001), primary tumor sites (p &amp;lt; 0.001) and HPV status (p &amp;lt; 0.001), and multivariate analysis associated the stromal subtype with a worse prognosis (HR = 1.5646, p = 0.006). We also observed several dysregulated miRNA families and clusters that function as regulators of subtype-specific gene expression networks in HNSCC. Conclusion: Our findings suggest miRNAs determine HNSCC subclassifications through coordinating growth and differentiation programs in epithelial cells. These results delineate developmental miRNA signatures characterizing the phenotypic diversity between HNSCC subtypes, providing an expanded framework for the pathogenesis and personalized treatment of HNSCC. Citation Format: Jeremiah R. Holt, Heejoon Jo, Vonn Walter, Xiaobei Zhao, David Neil Hayes, Yoon Ho Ko. Integrative analysis of microRNA expression identifies two biologically distinct and clinically relevant subtypes of head and neck squamous cell carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5448.

Abstract 4007: Integrative analysis of miRNAs classify two distinct stages of epithelial cell differentiation in head and neck squamous cell carcinoma (HNSCC)

Abstract Background Analyses of microRNA expression profiles have revealed that many microRNAs are expressed aberrantly and correlate with tumorigenesis, progression, and prognosis of various solid tumors. However, several miRNA analyses of head and neck squamous cell carcinoma (HNSCC) have been inconsistent among studies due to the small sample size. Method 366 HNSCC samples from two independent subsets of patients from UNC and The Cancer Genome Atlas (TCGA) were analyzed by the different platforms, microRNA microarray and miRNA Seq, respectively. Using the integrative correlations method, 41 miRNAs were selected as highly reliable across the different platforms. Tumor statistically significant subtypes were identified using consensus clustering and miRNA SigClust test statistic. miRNA clusters were validated across independent cohorts using centroids. Clinical and pathway associations of the subtypes were evaluated using logistic regression and gene ontology approaches. Results We identified two clinically relevant and genetically different subclasses of HNSCC that each related to a different stage of epithelial cell differentiation and were independently validated (P &amp;lt; 0.001). These were named epithelial and stromal subtypes according to their respective correlations with functional target gene ontology. Each subclass demonstrated significant differences in terms of mRNA signature (P &amp;lt; 0.001), primary tumor sites (P &amp;lt; 0.001), and a model of normal epithelial development. Multivariate analysis revealed that stromal subtype was independently associated with poor prognosis (hazard ratio of 1.677, P = 0.014.) We also found several microRNAs as strong regulators of subclass-specific gene expression networks in HNSCC. Among these miRNAs, the miR-200 family suppresses mesenchymal differentiation in HNSCC by downregulating expression of epithelial-mesenchymal transition. Conclusion Our findings assume that microRNAs are significant determinants of HNSCC subclass through their ability to regulate developmental growth and differentiation programs in epithelial cells. Taken together, our results delineate developmental microRNA expression signatures that both characterize and yield the phenotypic diversity of HNSCC subclasses, thus providing an expanded framework for understanding the pathogenesis of HNSCC. Note: This abstract was not presented at the meeting. Citation Format: Yoon Ho Ko, Vonn Walter, Michael Catalano, Xiaoying Yin, Patrick Kimes, Xiaobei Xiao Xiao, David Neil Hayes. Integrative analysis of miRNAs classify two distinct stages of epithelial cell differentiation in head and neck squamous cell carcinoma (HNSCC). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4007. doi:10.1158/1538-7445.AM2015-4007

Notch Signaling Modulates MUC16 Biosynthesis in an In Vitro Model of Human Corneal and Conjunctival Epithelial Cell Differentiation

Notch proteins are a family of transmembrane receptors that coordinate binary cell fate decisions and differentiation in wet-surfaced epithelia. We sought to determine whether Notch signaling contributes to maintaining mucosal homeostasis by modulating the biosynthesis of cell surface-associated mucins in an in vitro model of human corneal (HCLE) and conjunctival (HCjE) epithelial cell differentiation. HCLE and HCjE cells were grown at different stages of differentiation, representing nondifferentiated (preconfluent and confluent) and differentiated (stratified) epithelial cultures. Notch signaling was blocked with the γ-secretase inhibitor dibenzazepine (DBZ). The presence of Notch intracellular domains (Notch1 to Notch3) and mucin protein (MUC1, -4, -16) was evaluated by electrophoresis and Western blot analysis. Mucin gene expression was determined by TaqMan real-time polymerase chain reaction. Here we demonstrate that Notch3 is highly expressed in undifferentiated and differentiated HCLE and HCjE cells, and that Notch1 and Notch2 biosynthesis is enhanced by induction of differentiation with serum-containing media. Inhibition of Notch signaling with DBZ impaired MUC16 biosynthesis in a concentration-dependent manner in undifferentiated cells at both preconfluent and confluent stages, but not in postmitotic stratified cells. In contrast to protein levels, the amount of MUC16 transcripts were not significantly reduced after DBZ treatment, suggesting that Notch regulates MUC16 posttranscriptionally. Immunoblots of DBZ-treated epithelial cells grown at different stages of differentiation revealed no differences in the levels of MUC1 and MUC4. These results indicate that MUC16 biosynthesis is posttranscriptionally regulated by Notch signaling at early stages of epithelial cell differentiation, and suggest that Notch activation contributes to maintaining a mucosal phenotype at the ocular surface.