scholarly journals MACE RNA sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Stefaniya Boneva ◽  
Anja Schlecht ◽  
Peipei Zhang ◽  
Daniel Boehringer ◽  
Thabo Lapp ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Rna Sequencing ◽  
Expression Profile ◽  
Squamous Cell ◽  
Classification Model ◽  
Sequencing Analysis ◽  
Conjunctival Squamous Cell Carcinoma ◽  
Formalin Fixed

AbstractRecent advances in the field of biomedical research allow for elucidation of the transcriptional signature of rare tumors such as conjunctival squamous cell carcinoma (SCC). In this study we compare its expression profile to conjunctival papilloma (Pap) and healthy conjunctival tissue (Ctrl) and develop a classification tool to differentiate these entities. Seven conjunctival SCC, seven Pap and ten Ctrl were formalin-fixed and paraffin-embedded (FFPE) and analyzed using Massive Analysis of cDNA Ends (MACE) RNA sequencing. Differentially expressed genes (DEG) and gene ontology (GO) clusters were explored and the abundance of involved cell types was quantified by xCell. Finally, a classification model was developed to distinguish SCC from Pap and Ctrl. Among the most prominent DEG in SCC a plethora of keratins were upregulated when compared to Pap and Ctrl. xCell analysis revealed an enrichment of immune cells, including activated dendritic cells and T-helper type 1 cells (Th1), in SCC when compared to Ctrl. The generated classification model could reliably discriminate between the three entities according to the expression pattern of 30 factors. This study provides a transcriptome-wide gene expression profile of rare conjunctival SCC. The analysis identifies distinct keratins, as well as dendritic and Th1 cells as important mediators in SCC. Finally, the provided gene expression classifier may become an aid to the conventional histological classification of conjunctival tumors in uncertain cases.

Gene Expression Profile in Oral Squamous Cell Carcinoma: A Pilot Study

2005 ◽  
Vol 63 (6) ◽  
pp. 786-792 ◽  
Author(s):  
José Manuel Somoza-Martín ◽  
Abel García-García ◽  
Francisco Barros-Angueira ◽  
Eva Otero-Rey ◽  
María Torres-Español ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Pilot Study ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Squamous Cell

scholarly journals Altered gene expression in conjunctival squamous cell carcinoma

2016 ◽  
Vol 29 (5) ◽  
pp. 452-460 ◽  
Author(s):  
Alka Mahale ◽  
Hind Alkatan ◽  
Saeed Alwadani ◽  
Maha Othman ◽  
Maria J Suarez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Altered Gene Expression ◽  
Conjunctival Squamous Cell Carcinoma ◽  
Altered Gene

Fibroblast gene expression profile reflects the stage of tumour progression in oral squamous cell carcinoma

2011 ◽  
Vol 223 (4) ◽  
pp. 459-469 ◽  
Author(s):  
Kue Peng Lim ◽  
Nicola Cirillo ◽  
Yazan Hassona ◽  
Wenbin Wei ◽  
Johanna K Thurlow ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Squamous Cell ◽  
Tumour Progression

scholarly journals Analytical validity of DecisionDx-SCC, a gene expression profile test to identify risk of metastasis in cutaneous squamous cell carcinoma (SCC) patients

2021 ◽  
Author(s):  
Sherri Borman ◽  
Jeff Wilkinson ◽  
Lauren Meldi-Sholl ◽  
Clare Johnson ◽  
Kelsey Carter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
High Risk ◽  
Cell Carcinoma ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Squamous Cell ◽  
Cutaneous Squamous Cell Carcinoma ◽  
Risk Class ◽  
Class 1

Abstract Background To improve identification of patients with cutaneous squamous cell carcinoma (SCC) at high risk for metastatic disease, the DecisionDx-SCC assay, a prognostic 40-gene expression profile (40-GEP) test, was developed and validated. The 40-GEP assay utilizes RT-PCR gene expression analysis on primary tumor biopsy tissue to evaluate the expression of 34 signature gene targets and 6 normalization genes. The test provides classifications of low risk (Class 1), moderate risk (Class 2A), and high risk (Class 2B) of metastasis within 3 years of diagnosis. The primary objective of this study was to validate the analytical performance of the 40 gene expression signature. Methods The repeatability and reproducibility of the 40-GEP test was evaluated by performance of inter-assay, intra-assay, and inter-operator precision experiments along with monitoring the reliability of sample and reagent stability for class call concordance. The technical performance of clinical orders from September 2020 through July 2021 for the 40-GEP test was assessed. Results Patient hematoxylin and eosin (H&E) stained slides were reviewed by a board-certified pathologist to assess minimum acceptable tumor content. Class specific controls (Class 1 and Class 2B) were evaluated with Levey Jennings analysis and demonstrated consistent and reproducible results. Inter-assay, inter-operator and intra-assay concordance were all ≥90%, with short-term and long-term RNA stability also meeting minimum concordance requirements. Of the 2,446 orders received, 93.4% remained eligible for testing, with 96.8% of all tested samples that completed the assay demonstrating actionable class call results. Conclusion DecisionDx-SCC demonstrates a high degree of analytical precision, yielding high concordance rates across multiple performance experiments, along with exhibiting robust technical reliability on clinical samples.

scholarly journals Decoding the Genetic Alterations in PRAME Gene Family and Its Association with Head and Neck Squamous Cell Carcinoma

2020 ◽  
pp. 93-102
Author(s):  
J. Dhivyadharshini ◽  
A. S. Smiline Girija ◽  
A. Paramasivam ◽  
J. Vijayashree Priyadharsini
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Survival Rate ◽  
Gene Family ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Expression Profile ◽  
Squamous Cell ◽  
Genetic Alterations ◽  
Neck Squamous Cell Carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the most common form of cancer with an incidence rate greater in male than in female. Advancements in molecular diagnostics have identified several pathways which can have a direct or indirect role in the development and progression of HNSCC. The PRAME (PReferentially Antigen expressed in MElanoma) gene family is yet another group of genes which has been recently implicated in HNSCC. The present study aims to identify the genetic alterations, the pattern of gene expression and the consequence of mutations in the PRAME family of genes in HNSCC patients. Several databases such as cBioportal, gnomAD, IMutant, PROVEAN were used to assess genetic alterations. The alterations included deep deletions, amplification, inframe, missense, truncating mutations. The gene showing the highest frequency of alteration (PRAME - 3%) was further assessed for its gene expression profile using the UALCAN database. The expression profile relative to normal samples was found to be significantly higher in HNSCC patients (p = 1.11 x 10-16). Further, the survival curve based on high and low/medium expression of the PRAME gene was assessed by Kaplan-Meier method. The analysis revealed a significant difference in the survival rate of patients with high and low/medicum level expression (0.0095). In addition, the high level expression was found to be associated with poor survival rate in HNSCC patients compared to those exhibiting low and medium level expression. In conclusion the study provides insights into the putative association of genes of the PRAME family with HNSCC. The preliminary results have to be further validated using experimental procedures.

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