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Peer-reviewedCC BY-NC-NDClinical epigenetics

Bridging the gap: advanced chromatin biotechnologies for circadian epigenomic profiling in head and neck squamous cell carcinoma.

  • Sehrish Khan1,2,3
  • Raed Said2,4
  • Christopher Eskiw5
  • François Thuot4
  • Benoit Guay4
  • Petros Papagerakis6
  • Silvana Papagerakis7,8
8 affiliations
  1. 1Department of Neuroscience, Faculté de Médicine, Université Laval, Québec City, Québec, Canada.
  2. 2Interdisciplinary Center for Clinical and Applied Research and Entrepreneurship (I-CARE)/Centre Interdisciplinaire pour la recherche clinique et appliqué (CIRCA), Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada.
  3. 3Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
  4. 4Department of Oto-Rhino-Laryngology and Head and Neck Surgery, Faculty of Medicine, Université Laval, Québec City, Québec, Canada.
  5. 5Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
  6. 6Dental School, University of Melbourne, Melbourne, VIC, Australia. [email protected].
  7. 7Interdisciplinary Center for Clinical and Applied Research and Entrepreneurship (I-CARE)/Centre Interdisciplinaire pour la recherche clinique et appliqué (CIRCA), Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada. [email protected].
  8. 8Department of Oto-Rhino-Laryngology and Head and Neck Surgery, Faculty of Medicine, Université Laval, Québec City, Québec, Canada. [email protected].
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Abstract

Surgery, radiotherapy and chemotherapy remain the main therapies for treating head and neck cancers, however new modalities have emerged with an emphasis to understand the complexity of the tumor biology. One emerging layer of complexity is the circadian clock, disrupted in many cancers, contributes to pathogenesis and progression due to its crosstalk with cancer pathways. While transcriptional alterations of core clock genes have been described in Head and Neck squamous cell carcinoma (HNSCC), the higher-order epigenetic and chromatin-based mechanisms underlying circadian dysregulation remain poorly defined. In this review, we highlight the potential of several chromatin-based biotechnologies in characterizing circadian clock disruption and identifying epigenetic biomarkers in HNSCC. Powerful assays including Chromatin conformation capture, Chromatin immunoprecipitation, DNA methylation profiling, ATAC-seq and single cell technologies can dissect circadian disruption at multiple regulatory layers. These approaches enable genome-wide mapping of chromatin accessibility, histone modifications, and 3D chromatin organization. Integrating these approaches across HPV-positive (HPV+) and HPV-negative (HPV-) HNSCC provides a framework to determine whether circadian disruption reflects transcriptional deregulation alone or involved structural genome remodeling that actively drives tumor progression. Linking circadian disruption to epigenomic reprogramming in HNSCCs can serve to identify mechanisms of therapeutic resistance and identify vulnerabilities. Advancing chromatin-informed circadian biomarker discovery in HNSCC has the potential to shift precision oncology from static genomic profiling toward dynamic, architecture-based epigenetic regulation.

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Cite

BibTeXRIS
BibTeX
@article{khan2026bridging,
  title = {{Bridging the gap: advanced chromatin biotechnologies for circadian epigenomic profiling in head and neck squamous cell carcinoma.}},
  author = {Sehrish Khan and Raed Said and Christopher Eskiw and François Thuot and Benoit Guay and Petros Papagerakis and Silvana Papagerakis},
  journal = {Clinical epigenetics},
  year = {2026},
  month = jul,
  doi = {10.1186/s13148-026-02189-8},
  url = {https://europepmc.org/article/MED/42928351},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - Bridging the gap: advanced chromatin biotechnologies for circadian epigenomic profiling in head and neck squamous cell carcinoma.
AU  - Sehrish Khan
AU  - Raed Said
AU  - Christopher Eskiw
AU  - François Thuot
AU  - Benoit Guay
AU  - Petros Papagerakis
AU  - Silvana Papagerakis
PY  - 2026
DA  - 2026/07/28
JO  - Clinical epigenetics
DO  - 10.1186/s13148-026-02189-8
UR  - https://europepmc.org/article/MED/42928351
AB  - Surgery, radiotherapy and chemotherapy remain the main therapies for treating head and neck cancers, however new modalities have emerged with an emphasis to understand the complexity of the tumor biology. One emerging layer of complexity is the circadian clock, disrupted in many cancers, contributes to pathogenesis and progression due to its crosstalk with cancer pathways. While transcriptional alterations of core clock genes have been described in Head and Neck squamous cell carcinoma (HNSCC), the higher-order epigenetic and chromatin-based mechanisms underlying circadian dysregulation remain poorly defined. In this review, we highlight the potential of several chromatin-based biotechnologies in characterizing circadian clock disruption and identifying epigenetic biomarkers in HNSCC. Powerful assays including Chromatin conformation capture, Chromatin immunoprecipitation, DNA methylation profiling, ATAC-seq and single cell technologies can dissect circadian disruption at multiple regulatory layers. These approaches enable genome-wide mapping of chromatin accessibility, histone modifications, and 3D chromatin organization. Integrating these approaches across HPV-positive (HPV+) and HPV-negative (HPV-) HNSCC provides a framework to determine whether circadian disruption reflects transcriptional deregulation alone or involved structural genome remodeling that actively drives tumor progression. Linking circadian disruption to epigenomic reprogramming in HNSCCs can serve to identify mechanisms of therapeutic resistance and identify vulnerabilities. Advancing chromatin-informed circadian biomarker discovery in HNSCC has the potential to shift precision oncology from static genomic profiling toward dynamic, architecture-based epigenetic regulation.
SN  - 1868-7083
ER  -