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Cancers
Special Issues
Head and Neck Cancer Genomics and Translational Applications
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Head and Neck Cancer Genomics and Translational Applications

A special issue of Cancers (ISSN 2072-6694).

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 6740

Special Issue Editor

Dr. Sabrina Daniela da Silva

E-Mail Website
Guest Editor
Department of Otolaryngology–Head and Neck Surgery, McGill University, Montreal, QC H3T 1E2, Canada
Interests: carcinogenesis; cancer progression; metastasis signaling; preclinical and animal models; genetic, genomic and epigenomic; target and drug discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is noticeable that the number of new cases of head and neck cancer has been increasing rapidly in recent decades, especially among young adults. This is not only associated with tobacco and alcohol consumption, but due to HPV infection that has emerged as an additional risk factor, defining a new subtype of tumor that is distinct from “conventional” HPV‐negative ones. Head and neck cancer is remarkably heterogeneous, comprising several subtypes in different anatomic sites of the upper aerodigestive tracts (nasal cavity, oral cavity, oropharynx, pharynx, hypopharynx, and larynx) with complex pathological and molecular features. Despite the advances in medical imaging and therapeutic approaches, the outcome of patients with advanced head and neck cancer remains poor, and the 5‐years survival is stagnant at <50%. Indeed, the lack of flexibility in therapeutic strategies often leads to patients suffering from inadequate or excessive treatment with severe side effects and lifelong consequences.

Recent developments and improvements in high-throughput genomic sequencing and proteomic technologies have produced an enormous amount of data and advanced our knowledge of the etiology, treatment resistance, and potential biomarkers of head and neck cancers. However, translation of these data into clinical progress needs further improvements. This is one of the top priorities in the head and neck cancer field to revert the obscure scenario of poor outcomes and improve cancer treatment and patient survival. For this Special Issue, we welcome experts in basic translational science and clinical research to present and review all aspects of genomics and translational research in head and neck cancer and contribute to advance our field.

Dr. Sabrina Daniela da Silva
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cancers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • head and neck cancer
  • translational research
  • genomics
  • epigenetics
  • biomarker
  • molecular biology
  • prognosis
  • regenerative medicine
  • therapeutic decision-making
  • bioengineering

Published Papers (2 papers)

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Research

21 pages, 22257 KiB  
Article
3p Arm Loss and Survival in Head and Neck Cancer: An Analysis of TCGA Dataset
by Hugh Andrew Jinwook Kim, Mushfiq Hassan Shaikh, Mark Lee, Peter Y. F. Zeng, Alana Sorgini, Temitope Akintola, Xiaoxiao Deng, Laura Jarycki, Halema Khan, Danielle MacNeil, Mohammed Imran Khan, Adrian Mendez, John Yoo, Kevin Fung, Pencilla Lang, David A. Palma, Krupal Patel, Joe S. Mymryk, John W. Barrett, Paul C. Boutros, Luc G. T. Morris and Anthony C. Nicholsadd Show full author list remove Hide full author list
Cancers 2021, 13(21), 5313; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13215313 - 22 Oct 2021
Cited by 2 | Viewed by 2698
Abstract
Loss of the 3p chromosome arm has previously been reported to be a biomarker of poorer outcome in both human papillomavirus (HPV)-positive and HPV-negative head and neck cancer. However, the precise operational measurement of 3p arm loss is unclear and the mutational profile [...] Read more.
Loss of the 3p chromosome arm has previously been reported to be a biomarker of poorer outcome in both human papillomavirus (HPV)-positive and HPV-negative head and neck cancer. However, the precise operational measurement of 3p arm loss is unclear and the mutational profile associated with the event has not been thoroughly characterized. We downloaded the clinical, single nucleotide variation (SNV), copy number aberration (CNA), RNA sequencing, and reverse phase protein assay (RPPA) data from The Cancer Genome Atlas (TCGA) and The Cancer Proteome Atlas HNSCC cohorts. Survival data and hypoxia scores were downloaded from published studies. In addition, we report the inclusion of an independent Memorial Sloan Kettering cohort. We assessed the frequency of loci deletions across the 3p arm separately in HPV-positive and -negative disease. We found that deletions on chromosome 3p were almost exclusively an all or none event in the HPV-negative cohort; patients either had <1% or >97% of the arm deleted. 3p arm loss, defined as >97% deletion in HPV-positive patients and >50% in HPV-negative patients, had no impact on survival (p > 0.05). However, HPV-negative tumors with 3p arm loss presented at a higher N-category and overall stage and developed more distant metastases (p < 0.05). They were enriched for SNVs in TP53, and depleted for point mutations in CASP8, HRAS, HLA-A, HUWE1, HLA-B, and COL22A1 (false discovery rate, FDR < 0.05). 3p arm loss was associated with CNAs across the whole genome (FDR < 0.1), and pathway analysis revealed low lymphoid–non-lymphoid cell interactions and cytokine signaling (FDR < 0.1). In the tumor microenvironment, 3p arm lost tumors had low immune cell infiltration (FDR < 0.1) and elevated hypoxia (FDR < 0.1). 3p arm lost tumors had lower abundance of proteins phospho-HER3 and ANXA1, and higher abundance of miRNAs hsa-miR-548k and hsa-miR-421, which were all associated with survival. There were no molecular differences by 3p arm status in HPV-positive patients, at least at our statistical power level. 3p arm loss is largely an all or none phenomenon in HPV-negative disease and does not predict poorer survival from the time of diagnosis in TCGA cohort. However, it produces tumors with distinct molecular characteristics and may represent a clinically useful biomarker to guide treatment decisions for HPV-negative patients. Full article
(This article belongs to the Special Issue Head and Neck Cancer Genomics and Translational Applications)
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17 pages, 2085 KiB  
Article
DNA Methylation Markers from Negative Surgical Margins Can Predict Recurrence of Oral Squamous Cell Carcinoma
by Bruna Pereira Sorroche, Fazlur Rahman Talukdar, Sheila Coelho Soares Lima, Matias Eliseo Melendez, Ana Carolina de Carvalho, Gisele Caravina de Almeida, Pedro De Marchi, Monique Lopes, Luis Felipe Ribeiro Pinto, André Lopes Carvalho, Zdenko Herceg and Lidia Maria Rebolho Batista Arantes
Cancers 2021, 13(12), 2915; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13122915 - 11 Jun 2021
Cited by 11 | Viewed by 3260
Abstract
The identification of molecular markers in negative surgical margins of oral squamous cell carcinoma (OSCC) might help in identifying residual molecular aberrations, and potentially improve the prediction of prognosis. We performed an Infinium MethylationEPIC BeadChip array on 32 negative surgical margins stratified based [...] Read more.
The identification of molecular markers in negative surgical margins of oral squamous cell carcinoma (OSCC) might help in identifying residual molecular aberrations, and potentially improve the prediction of prognosis. We performed an Infinium MethylationEPIC BeadChip array on 32 negative surgical margins stratified based on the status of tumor recurrence in order to identify recurrence-specific aberrant DNA methylation (DNAme) markers. We identified 2512 recurrence-associated Differentially Methylated Positions (DMPs) and 392 Differentially Methylated Regions (DMRs) which were enriched in cell signaling and cancer-related pathways. A set of 14-CpG markers was able to discriminate recurrent and non-recurrent cases with high specificity and sensitivity rates (AUC 0.98, p = 3 × 10−6; CI: 0.95–1). A risk score based on the 14-CpG marker panel was applied, with cases classified within higher risk scores exhibiting poorer survival. The results were replicated using tumor-adjacent normal HNSCC samples from The Cancer Genome Atlas (TCGA). We identified residual DNAme aberrations in the negative surgical margins of OSCC patients, which could be informative for patient management by improving therapeutic intervention. This study proposes a novel DNAme-based 14-CpG marker panel as a promising predictor for tumor recurrence, which might contribute to improved decision-making for the personalized treatment of OSCC cases. Full article
(This article belongs to the Special Issue Head and Neck Cancer Genomics and Translational Applications)
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