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Using Microarrays to Interrogate Microenvironmental Impact on Cellular Phenotypes in Cancer
Published on: May 21, 2019
Developing the Role of a Multigene Panel in BMSCC: Tumor Microenvironment Impact and Clinical Applications
Kinjal D Patel1, Vaidehi P Thakore1, Ashi R Thobias1
1Cancer Biology Department, The Gujarat Cancer & Research Institute (GCRI), Ahmedabad, Gujarat, India.
Background:
Buccal mucosa squamous cell carcinoma (BMSCC), a prevalent oral cancer in India, presenting late, leads to high recurrence rates and poor survival. This study aimed to develop a multigene panel for BMSCC diagnosis and prognosis.
Methods:
Gene-expression profiling was performed on FFPE tissues (discovery cohort: BMSCC = 135, normal = 31) using Agilent SurePrint G3 human gene-expression v3 microarray chips. The top 1000 altered genes were further analyzed for gene ontology, pathways, and protein-protein interaction.
Results:
Twenty four-gene panel was developed, selected for its role in prognosis. Virtual validation using TCGA cohorts confirmed dysregulation in nearly all genes. Fifteen genes correlated with poor prognosis in TCGA. qRT-PCR analysis in clinical cohort (BMSCC = 50, normal = 50) showed significant alterations in 22 genes. Receiver operating characteristic curve analysis identified 11 genes with > 80% diagnostic accuracy. Predictive models generated through principal component analysis and combined-ROC analysis ensured accuracy and reliability.
Conclusions:
This multigene panel depicts strong diagnostic and prognostic potential for BMSCC.
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