Amrita Jay

Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors

BackgroundHuman papillomavirus positive (HPV+) head and neck squamous cell carcinoma (HNSCC) is an emerging disease, representing a distinct clinical and epidemiological entity. Understanding the genetic basis of this specific subtype of cancer could allow therapeutic targeting of affected pathways for a stratified medicine approach.MethodsTwenty HPV+ and 20 HPV- laser-capture microdissected oropharyngeal carcinomas were used for paired-end sequencing of hybrid-captured DNA, targeting 3,230 exons in 182 genes often mutated in cancer. Copy number alteration (CNA) profiling, Sequenom MassArray sequencing and immunohistochemistry were used to further validate findings.ResultsHPV+ and HPV- oropharyngeal carcinomas cluster into two distinct subgroups. TP53 mutations are detected in 100% of HPV negative cases and abrogation of the G1/S checkpoint by CDKN2A/B deletion and/or CCND1 amplification occurs in the majority of HPV- tumors.ConclusionThese findings strongly support a causal role for HPV, acting via p53 and RB pathway inhibition, in the pathogenesis of a subset of oropharyngeal cancers and suggest that studies of CDK inhibitors in HPV- disease may be warranted. Mutation and copy number alteration of PI3 kinase (PI3K) pathway components appears particularly prevalent in HPV+ tumors and assessment of these alterations may aid in the interpretation of current clinical trials of PI3K, AKT, and mTOR inhibitors in HNSCC.

Identification and functional validation of HPV-mediated hypermethylation in head and neck squamous cell carcinoma

BackgroundHuman papillomavirus-positive (HPV+) head and neck squamous cell carcinoma (HNSCC) represents a distinct clinical and epidemiological condition compared with HPV-negative (HPV-) HNSCC. To test the possible involvement of epigenetic modulation by HPV in HNSCC, we conducted a genome-wide DNA-methylation analysis.MethodsUsing laser-capture microdissection of 42 formalin-fixed paraffin wax-embedded (FFPE) HNSCCs, we generated DNA-methylation profiles of 18 HPV+ and 14 HPV- samples, using Infinium 450 k BeadArray technology. Methylation data were validated in two sets of independent HPV+/HPV- HNSCC samples (fresh-frozen samples and cell lines) using two independent methods (Infinium 450 k and whole-genome methylated DNA immunoprecipitation sequencing (MeDIP-seq)). For the functional analysis, an HPV- HNSCC cell line was transduced with lentiviral constructs containing the two HPV oncogenes (E6 and E7), and effects on methylation were assayed using the Infinium 450 k technology.Results and discussionUnsupervised clustering over the methylation variable positions (MVPs) with greatest variation showed that samples segregated in accordance with HPV status, but also that HPV+ tumors are heterogeneous. MVPs were significantly enriched at transcriptional start sites, leading to the identification of a candidate CpG island methylator phenotype in a sub-group of the HPV+ tumors. Supervised analysis identified a strong preponderance (87%) of MVPs towards hypermethylation in HPV+ HNSCC. Meta-analysis of our HNSCC and publicly available methylation data in cervical and lung cancers confirmed the observed DNA-methylation signature to be HPV-specific and tissue-independent. Grouping of MVPs into functionally more significant differentially methylated regions identified 43 hypermethylated promoter DMRs, including for three cadherins of the Polycomb group target genes. Integration with independent expression data showed strong negative correlation, especially for the cadherin gene-family members. Combinatorial ectopic expression of the two HPV oncogenes (E6 and E7) in an HPV- HNSCC cell line partially phenocopied the hypermethylation signature seen in HPV+ HNSCC tumors, and established E6 as the main viral effector gene.ConclusionsOur data establish that archival FFPE tissue is very suitable for this type of methylome analysis, and suggest that HPV modulates the HNSCC epigenome through hypermethylation of Polycomb repressive complex 2 target genes such as cadherins, which are implicated in tumor progression and metastasis.

In vitro examination of suspicious oral lesions using optical coherence tomography

We compared findings of optical coherence tomography (OCT) with histopathological results of suspicious oral lesions to assess the feasibility of using OCT to identify malignant tissue. Thirty-four oral lesions from 27 patients had swept-source frequency-domain OCT. Four variables were assessed (changes in keratin, epithelial, and sub-epithelial layers, and identification of the basement membrane) and from this we calculated whether or not there were architectural changes. These data were then compared with histopathological results. Two clinicians, who were unaware of the clinical and histopathological diagnoses, decided whether biopsy was necessary. The basement membrane was recognised in only 15 oral lesions. OCT could identify diseased areas but could not provide a diagnosis or differentiate between lesions. The two clinicians, who recommended biopsy agreed in all cases. This pilot study confirms the feasibility of using OCT to identify architectural changes in malignant tissues.

Structural validation of oral mucosal tissue using optical coherence tomography

BackgroundOptical coherence tomography (OCT) is a non-invasive optical technology using near-infrared light to produce cross-sectional tissue images with lateral resolution.ObjectivesThe overall aims of this study was to generate a bank of normative and pathological OCT data of the oral tissues to allow identification of cellular structures of normal and pathological processes with the aim to create a diagnostic algorithm which can be used in the early detection of oral disorders.Material and methodsSeventy-three patients with 78 suspicious oral lesions were referred for further management to the UCLH Head and Neck Centre, London. The entire cohort had their lesions surgically biopsied (incisional or excisional). The immediate ex vivo phase involved scanning the specimens using optical coherence tomography. The specimens were then processed by a histopathologist.Five tissue structures were evaluated as part of this study, including: keratin cell layer, epithelial layer, basement membrane, lamina propria and other microanatomical structures. Two independent assessors (clinician and pathologist trained to use OCT) assessed the OCT images and were asked to comment on the cellular structures and changes involving the five tissue structures in non-blind fashion.ResultsCorrect identification of the keratin cell layer and its structural changes was achieved in 87% of the cohort; for the epithelial layer it reached 93.5%, and 94% for the basement membrane. Microanatomical structures identification was 64% for blood vessels, 58% for salivary gland ducts and 89% for rete pegs. The agreement was “good” between the clinician and the pathologist.OCT was able to differential normal from pathological tissue and pathological tissue of different entities in this immediate ex vivo study. Unfortunately, OCT provided inadequate cellular and subcellular information to enable the grading of oral premalignant disorders.ConclusionThis study enabled the creation of OCT bank of normal and pathological oral tissues. The pathological changes identified using OCT enabled differentiation between normal and pathological tissues, and identification of different tissue pathologies.Further studies are required to assess the accuracy of OCT in identification of various pathological processes involving the oral tissues.

Salivary gland FNA cytology: role as a triage tool and an approach to pitfalls in cytomorphology.

To highlight the importance of salivary gland fine needle aspiration (FNA) cytology as a triage tool for surgery and to determine its sensitivity and specificity. To discuss the diagnostic pitfalls and potential role of ancillary techniques in diagnosis and prognosis.

Integrated virus-host methylome analysis in head and neck squamous cell carcinoma

One in six cancers worldwide is caused by infection and human papillomavirus (HPV) is one of the main culprits. To better understand the dynamics of HPV integration and its effect on both the viral and host methylomes, we conducted whole-genome DNA methylation analysis using MeDIP-seq of HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC). We determined the viral subtype to be HPV-16 in all cases and show that HPV-16 integrates into the host genome at multiple random sites and that this process predominantly involves the transcriptional repressor gene (E2) in the viral genome. Comparative analysis identified 453 (FDR ≤ 0.01) differentially methylated regions (DMRs) in the HPV+ host methylome. Bioinformatics characterization of these DMRs confirmed the previously reported cadherin genes to be affected but also revealed new targets for HPV-mediated methylation changes at regions not covered by array-based platforms, including the recently identified super-enhancers.

Carcinoma Cuniculatum Arising in the Tongue

Carcinoma cuniculatum (CC) is a rare, distinct clinico-pathological variant of squamous cell carcinoma (SCC) that is defined histologically by the characteristic infiltrative pattern of a deep, broad, and complex proliferation of stratified squamous epithelium with keratin cores and keratin-filled crypts. Herein, we present a case report of CC of the oral tongue and discuss its diagnosis, management, and outcome, as well as briefly review the world literature. To our knowledge, this is the first documented case of CC of the tongue to be reported in the English literature. We draw attention to its clinico-pathological features and highlight that awareness of this entity as a distinct variant of SCC facilitates its correct management.

Multicentric human papillomavirus-associated head and neck squamous cell carcinoma

The purpose of this study was to present the clinicopathological features of a series of patients with human papillomavirus (HPV)‐associated head and neck second primary tumors.

Assessment of tumour resection margins using optical coherence tomography

In the treatment of cancer, the fundamental surgical goal is to remove all local malignant disease and leave no residual malignant cells. Studies have demonstrated the benefit of achieving negative resection margins in terms of disease free local recurrence and overall survival. The surgical margins for head & neck cancer may vary widely depending on the site of disease. Optical coherence tomography (OCT) is an imaging modality that uses light to determine cross-sectional anatomy in turbid media such as living tissues. In this study, we used this technology to evaluate resection margins acquired from patients with oral squamous cell cancer (OSCC).

Head and neck sarcomas: A single institute series

BACKGROUND Sarcomas are tumours of mesenchymal origin, accounting for 1% of all malignancies. METHODS This is a retrospective analysis of 107 head and neck sarcoma cases, treated over a period of thirteen years. RESULTS Fifty-four patients had with craniofacial bone sarcomas (BSs) (male: 33; female: 21) with high grade osteosarcoma being the most predominant type. The soft tissue sarcomas (STS) (53 patients; male: 28, female: 25) were histologically diverse with rhabdomyosarcomas and myxofibrosarcomas being the predominant types. The majority of BSs were managed with neoadjuvant chemotherapy followed by surgery, whereas in STSs treatment included predominantly surgery followed by radiotherapy. Overall survival estimates were 79% at 2years and 64% at 5years (mean follow-up period was 48months). CONCLUSIONS The mesenchymal origin of sarcomas, the pattern of disease spread and the different extent of cancellous bone infiltration in contrast to epithelial tumours, dictate distinct principles for surgical clearance.