Tumoral Versus Luminal Microbiome in Head and Neck Squamous Cell Carcinoma

Tumoral Versus Luminal Microbiome in Head and Neck Squamous Cell Carcinoma

Head and neck squamous cell carcinoma (HNSCC), France's 5th most common cancer (15,000 annual cases), presents significant public health challenges due to high morbidity and functional/aesthetic sequelae from treatments (mutilating surgery, radiotherapy, chemotherapy). Major risk factors, tobacco and alcohol, create a chronic inflammatory environment promoting tumor development. The upper aerodigestive tract microbiome, influenced by these exposures and local alterations (necrosis, bleeding, ulcerations), is emerging as a potential factor in tumor progression, severity biomarker, or therapeutic target, though its exact role (cause or consequence) remains to be elucidated

Objectives:

• Primary: Compare bacterial microbiome composition between tumor tissue, adjacent healthy mucosa, and pharyngeal secretions
• Secondary:
• Correlate microbiome diversity/composition with clinical and epidemiological characteristics
• Identify microbiome variations by tumor stage, histology, and infiltration
• Discover diagnostic/prognostic microbial markers
• Analyze somatic variants (SNP/CNV) via whole-genome sequencing (WGS) and their association with microbiome profiles and clinical parameters

Study Design: Prospective, cross-sectional study with paired design (each patient serves as their own control to minimize genetic variation biases)

Methods:

• Samples: Tumor, adjacent healthy tissue, and pharyngeal secretions (3 samples/patient)
• Sequencing: Metagenomic sequencing (complete bacterial genomes) when biomass permits, or targeted 16S rRNA sequencing to identify dominant genera.
• Pilot study: 20 patients to select the optimal technique and validate feasibility, particularly assessing DNA quantity in these low-biomass environments

Population: Adults with suspected HNSCC scheduled for panendoscopy

Exclusion criteria: Recent antibiotics/corticosteroids (12 weeks), immunosuppression (uncontrolled HIV, active hematologic malignancies, autoimmune diseases on immunosuppressants, organ/stem cell transplants, uncontrolled diabetes), immunomodulatory treatments (3 months), recurrence, pregnancy, non-French speakers, legal guardianship, or lack of social security.

Safety: No additional risks beyond standard panendoscopy.

Expected impact: This approach may pave the way for innovative diagnostic or therapeutic strategies based on microbiome modulation in HNSCC.

Inclusion Criteria:

• Adult patient
• Consultation in the ENT department for suspected squamous cell carcinoma of the upper aerodigestive tract scheduled for panendoscopy
• Patient has provided consent to participate in the study and signed an informed consent form

Exclusion Criteria:

• Antibiotic or corticosteroid therapy within 12 weeks prior to consultation

• Conditions associated with immunosuppression:

  • Uncontrolled HIV infection (CD4 < 200 cells/µL) (permanent exclusion)
  • Hematologic malignancies currently under treatment or not in complete remission for <2 years
  • Autoimmune diseases under immunosuppressive treatment
  • Solid organ or stem cell transplant recipients (permanent exclusion)
  • Poorly controlled diabetes (HbA1c > 9%)

• Immunomodulatory treatment within 3 months prior to consultation:

  • Immune checkpoint inhibitors (e.g., anti-PD-1/PD-L1, anti-CTLA-4)
  • Biotherapy targeting the immune system (anti-TNF, anti-IL, calcineurin inhibitors, antimetabolites)
  • Recurrent upper aerodigestive tract cancer previously treated with surgery and/or radiochemotherapy
  • Pregnancy (confirmed prior to panendoscopy)
  • Patient who does not speak or understand French
  • Subject under guardianship or curatorship
  • Subject not affiliated with the national health insurance system