CT Imaging Correlates of Genomic Expression for Oral Cavity Squamous Cell Carcinoma

Pickering, Curtis R.; Shah, Kanisha; Ahmed, Syed Adeel; Rao, Arvind; Frederick, Mitchell J.; Zhang, J.; Unruh, Anna K.; Wang, J.; Ginsberg, Lawrence E.; Kumar, Arvind; Myers, Jeffrey N.; Hamilton, Jackson

doi:10.3174/ajnr.a3635

Cited by 9 publications

(8 citation statements)

References 24 publications

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“…Likewise a missense change, p.T1010I (rs56391007, COSM707), in the MET gene was identified in one of our HPV-negative tumors. Although this change has been reported as a somatic mutation previously in other cancers [29,30], it has not been reported in the TCGA HNSCC dataset and is suspected to be a constitutional polymorphism in the individual from which this tumor was derived based on the variant frequency being within the range of 40-60 %. We were unable to acquire additional material (i.e.…”

Section: Mutation Profilingmentioning

confidence: 79%

Mutation and Transcriptional Profiling of Formalin-Fixed Paraffin Embedded Specimens as Companion Methods to Immunohistochemistry for Determining Therapeutic Targets in Oropharyngeal Squamous Cell Carcinoma (OPSCC): A Pilot of Proof of Principle

Saba

Wilson

Doho

et al. 2014

Head and Neck Pathol

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The role of molecular methods in the diagnosis of head and neck cancer is rapidly evolving and holds great potential for improving outcomes for all patients who suffer from this diverse group of malignancies. However, there is considerable debate as to the best clinical approaches, particularly for Next Generation Sequencing (NGS). The choices of NGS methods such as whole exome, whole genome, whole transcriptomes (RNA-Seq) or multiple gene resequencing panels, each have strengths and weakness based on data quality, the size of the data, the turnaround time for data analysis, and clinical actionability. There have also been a variety of gene expression signatures established from microarray studies that correlate with relapse and response to treatment, but none of these methods have been implemented as standard of care for oropharyngeal squamous cell carcinoma (OPSCC). Because many genomic methodologies are still far from the capabilities of most clinical laboratories, we chose to explore the use of a combination of off the shelf targeted mutation analysis and gene expression analysis methods to complement standard anatomical pathology methods. Specifically, we have used the Ion Torrent AmpliSeq cancer panel in combination with the NanoString nCounter Human Cancer Reference Kit on 8 formalin-fixed paraffin embedded (FFPE) OPSCC tumor specimens, (4) HPVpositive and (4) HPV-negative. Differential expression analysis between HPV-positive and negative groups showed that expression of several genes was highly likely to correlate with HPV status. For example, WNT1, PDGFA and OGG1 were all over-expressed in the positive group. Our results show the utility of these methods with routine FFPE clinical specimens to identify potential therapeutic targets which could be readily applied in a clinical trial setting for clinical laboratories lacking the instrumentation or bioinformatics infrastructure to support comprehensive genomics workflows. To the best of our knowledge, these preliminary experiments are among the earliest to combine both mutational and gene expression profiles using Ion Torrent and NanoString technologies. This reports serves as a proof of principle methodology in OPSCC.Electronic supplementary material The online version of this article

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Section: Mutation Profilingmentioning

confidence: 79%

Mutation and Transcriptional Profiling of Formalin-Fixed Paraffin Embedded Specimens as Companion Methods to Immunohistochemistry for Determining Therapeutic Targets in Oropharyngeal Squamous Cell Carcinoma (OPSCC): A Pilot of Proof of Principle

Saba

Wilson

Doho

et al. 2014

Head and Neck Pathol

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“…In paraganglioma, four studies found higher PET SUV-values for SDHx -mutated tumors [ 152 – 154 ] or SHDx and VHL -mutated tumors [ 155 ], relevant for heritability risk assessment. In head neck tumors, EGFR -expression was related to CT invasion, mass effect, size/volume [ 156 ] and lower capillary permeability on perfusion CT [ 157 ]. Additionally, 14 studies each reported on radiogenomic associations of 14 other malignancies, respectively (Table 3 ).…”

Section: Resultsmentioning

confidence: 99%

“…tumor size, multifocality) of both MRI and CT in various malignancies. Results included the correlations of enhancement features with VEGF -expression in brain tumors (glioblastoma) [ 158 ] and head-neck tumors (oral cavity SCC) [ 156 ].…”

Section: Resultsmentioning

confidence: 99%

Non-invasive tumor genotyping using radiogenomic biomarkers, a systematic review and oncology-wide pathway analysis

et al. 2018

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With targeted treatments playing an increasing role in oncology, the need arises for fast non-invasive genotyping in clinical practice. Radiogenomics is a rapidly evolving field of research aimed at identifying imaging biomarkers useful for non-invasive genotyping. Radiogenomic genotyping has the advantage that it can capture tumor heterogeneity, can be performed repeatedly for treatment monitoring, and can be performed in malignancies for which biopsy is not available. In this systematic review of 187 included articles, we compiled a database of radiogenomic associations and unraveled networks of imaging groups and gene pathways oncology-wide. Results indicated that ill-defined tumor margins and tumor heterogeneity can potentially be used as imaging biomarkers for 1p/19q codeletion in glioma, relevant for prognosis and disease profiling. In non-small cell lung cancer, FDG-PET uptake and CT-ground-glass-opacity features were associated with treatment-informing traits including EGFR-mutations and ALK-rearrangements. Oncology-wide gene pathway analysis revealed an association between contrast enhancement (imaging) and the targetable VEGF-signalling pathway. Although the need of independent validation remains a concern, radiogenomic biomarkers showed potential for prognosis prediction and targeted treatment selection. Quantitative imaging enhanced the potential of multiparametric radiogenomic models. A wealth of data has been compiled for guiding future research towards robust non-invasive genomic profiling.

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“…Multidetector computed tomography (CT) is among the most important examinations when diagnosing and staging oral and oropharyngeal cancers [2,3]. Tumor enhancement and the degree of mass effect on contrast-enhanced CT imaging reportedly correlate with genomic biomarkers that are potential drug targets [4]. Although a direct endoscopic examination can accurately evaluate tumors on the mucosal surface, the submucosal tumor extension and vascularity cannot be evaluated.…”

Section: Introductionmentioning

confidence: 99%

“…Although a direct endoscopic examination can accurately evaluate tumors on the mucosal surface, the submucosal tumor extension and vascularity cannot be evaluated. Therefore, CT is essential for evaluating head and neck cancers, and pretreatment CT has significantly improved the long-term management of and therapeutic strategy for patients with oral cavity cancers [1,4]. However, the CT image quality in the oral cavity often suffers from artifacts caused by metallic materials [5].…”

Section: Introductionmentioning

confidence: 99%

Added value of a single-energy projection-based metal-artifact reduction algorithm for the computed tomography evaluation of oral cavity cancers

et al. 2015

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CT Imaging Correlates of Genomic Expression for Oral Cavity Squamous Cell Carcinoma

Cited by 9 publications

References 24 publications

Mutation and Transcriptional Profiling of Formalin-Fixed Paraffin Embedded Specimens as Companion Methods to Immunohistochemistry for Determining Therapeutic Targets in Oropharyngeal Squamous Cell Carcinoma (OPSCC): A Pilot of Proof of Principle

Mutation and Transcriptional Profiling of Formalin-Fixed Paraffin Embedded Specimens as Companion Methods to Immunohistochemistry for Determining Therapeutic Targets in Oropharyngeal Squamous Cell Carcinoma (OPSCC): A Pilot of Proof of Principle

Non-invasive tumor genotyping using radiogenomic biomarkers, a systematic review and oncology-wide pathway analysis

Added value of a single-energy projection-based metal-artifact reduction algorithm for the computed tomography evaluation of oral cavity cancers

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