A Guide to Biomarkers for Lip, Oral Cavity, and Pharyngeal Cancers

When cancers start in the lip, oral cavity, or pharynx, we group them as head and neck squamous cell carcinomas. Same general family, very different neighborhoods. A tumor on the tongue behaves differently from one at the tonsil or behind the nose. Biomarkers help us read those differences clearly. They are measurable signals in the tumor or blood that refine diagnosis, stage disease more accurately, predict response to therapy, and help track for recurrence. In practical terms, they are the "map and compass" your care team uses to make smarter decisions with less guesswork.

What counts as a biomarker here?

Three categories show up again and again in lip, oral cavity, and pharyngeal cancers:

• Viral biomarkers that indicate HPV or EBV involvement
• Immune biomarkers that forecast benefit from immunotherapy
• Tumor genomic and liquid biopsy biomarkers that reveal vulnerabilities or help with monitoring

Each has a distinct job. Some are routine standards in guidelines. Others are promising but still maturing. I'll walk you through what's clinically useful now and where the evidence is headed.

HPV and p16: the oropharynx's signature biomarker

If a cancer begins in the oropharynx (tonsil, base of tongue, soft palate), we test the tumor for human papillomavirus (HPV) involvement. The workhorse test is p16 immunohistochemistry. When HPV oncoproteins (E6 and E7) inactivate the cell's GPS (p53) and brakes (Rb), the cell compensates by cranking up p16. A strong, diffuse p16 signal in tumor cells is a reliable surrogate for transcriptionally active HPV.¹

Why it matters:

• It changes staging. The AJCC 8th edition created a separate staging system for p16-positive oropharyngeal cancers because they behave more favorably than HPV-negative disease.²
• It refines prognosis. In multiple cohorts, p16-positive oropharyngeal cancers have higher response rates and survival compared with HPV-negative cancers, even at the same anatomic stage.³
• It guides trials. Many de-escalation studies explore whether p16-positive disease can be treated with similar cure rates and fewer long-term side effects. This research is active, though not all de-intensified approaches are standard of care.⁴

Important nuance: p16 testing is recommended for oropharyngeal primaries. For cancers of the oral cavity (e.g., tongue tip, floor of mouth, buccal mucosa) or larynx, p16 is not considered a reliable marker of HPV-driven biology and is not routinely used to guide care. If p16 and true HPV status disagree, pathologists may add HPV DNA or RNA in situ hybridization to clarify.⁵

EBV DNA: the nasopharyngeal tracker

Nasopharyngeal carcinoma (NPC), which sits behind the nose and above the soft palate, is tightly linked to Epstein–Barr virus in endemic regions. Plasma EBV DNA measured by quantitative PCR has become a powerful clinical tool.⁶

Where EBV DNA helps:

• Diagnosis and baseline risk. Detectable plasma EBV DNA at diagnosis supports NPC and correlates with tumor burden.
• Treatment monitoring. Levels often drop quickly with effective therapy and can rise before imaging picks up recurrence.⁷
• Surveillance. In endemic areas, EBV DNA has been used for population screening and post-treatment follow-up, with studies showing earlier detection of relapse, though real-world performance depends on assay quality and clinical context.

Caveats: Not all NPC is EBV-driven, especially outside endemic regions, and assay standardization varies. Reactivation of EBV from non-cancer causes can occasionally elevate levels. Your lab's method, reference ranges, and sample handling practices matter to interpretation.⁶

PD-L1 and the immunotherapy window

Programmed death-ligand 1 (PD-L1) expression doesn't diagnose head and neck cancer, but it helps predict benefit from immune checkpoint inhibitors in the recurrent or metastatic setting. Pathologists report a Combined Positive Score (CPS) using validated assays like 22C3 that count PD-L1 staining in both tumor and nearby immune cells, normalized to tumor cell number.⁸

How PD-L1 is used:

• CPS thresholds help determine eligibility for immunotherapy, either alone or with chemotherapy, based on large randomized trials and guidelines.⁸
• Higher CPS generally aligns with higher response rates, though responses can occur at low CPS and some high-CPS tumors do not respond.

Limitations and quality notes:

• PD-L1 is dynamic. It can vary by biopsy location, prior treatment, and time.
• Different antibody clones and scoring methods are not interchangeable. For decision-making, ensure the report specifies the assay and CPS.

MSI, TMB, and rare fusions: valuable when present

Most lip, oral cavity, and pharyngeal cancers do not show mismatch repair deficiency or MSI-high status, but when they do, it flags a DNA repair problem that creates abundant neoantigens. Those tumors tend to respond better to checkpoint blockade across cancer types.⁹ Tumor mutational burden (TMB) is similar conceptually. A high TMB may predict immunotherapy benefit, though cutoffs and assays vary by lab.⁹

Actionable gene fusions, such as NTRK fusions, are uncommon but meaningful. If present, they open targeted therapy options.¹⁰ Other mutations like TP53, PIK3CA, NOTCH1, HRAS, and TERT promoter changes are frequent in head and neck cancers but rarely change frontline treatment today outside of clinical trials. EGFR overexpression is common; EGFR mutations are rare. Unlike some lung cancers, routine EGFR mutation testing is not part of standard head and neck pathways.

What "next-generation sequencing" adds

Comprehensive genomic profiling (NGS) of tumor tissue is often considered for recurrent or metastatic disease. Here's what it can reveal:

• Eligibility for targeted therapies if a rare driver (e.g., NTRK fusion) is found¹¹
• MSI/MMR status and TMB, which inform immunotherapy discussions
• Clinical trial matches based on a tumor's molecular fingerprint

Realistic expectations: For most patients with head and neck squamous cell carcinoma, NGS will map the biology without producing an immediate drug target. That map is still valuable for surveillance strategies, prognostic context, and clinical trial planning.

Liquid biopsy and saliva: promising, with selective current uses

Liquid biopsy measures tumor-derived DNA shed into blood. In head and neck cancers, two applications are gaining practical traction:

• Plasma EBV DNA for NPC, as above
• HPV circulating tumor DNA (ctDNA) for HPV-positive oropharyngeal cancer, particularly for surveillance after curative therapy¹²

HPV ctDNA assays can pick up molecular recurrence before scans or symptoms. Several studies show that a rising HPV ctDNA signal after treatment predicts relapse risk.¹² These tests are not yet universal standard of care everywhere, but they are increasingly used in specialized centers because they can shift the timing of imaging or biopsy in a patient-centered way.

Salivary tests for HPV DNA, tumor DNA methylation, or panels of RNA/proteins are under active investigation.¹³ They're attractive because saliva sits right next to these tumors. For now, they're mostly research tools or adjuncts rather than guideline-backed standalones.

Putting biomarkers to work across the care journey

1) Diagnosis and staging

The first step is a tissue diagnosis. A pathologist confirms squamous cell carcinoma and the anatomic site. Then, the site guides biomarker selection.

• Oropharynx: p16 immunohistochemistry is routine. If needed, HPV DNA or RNA methods confirm.
• Nasopharynx: EBV testing is often incorporated, with plasma EBV DNA at baseline and during care.
• Oral cavity or lip: Focus remains on surgical pathology and margin status. HPV testing is not routinely recommended to guide care.

Imaging provides stage, but for p16-positive oropharyngeal cancer, stage grouping uses a different framework that better reflects the biology. That reclassification can change the risk conversation at the very first visit.²

2) Prognosis

Biomarkers refine the "how will this likely behave" question:

• HPV/p16 positivity in oropharyngeal cancer predicts better responses and survival compared with HPV-negative disease.³
• High baseline plasma EBV DNA in nasopharyngeal cancer is associated with higher tumor burden and relapse risk, while a rapid decline during therapy is favorable.
• General inflammatory markers (like neutrophil-to-lymphocyte ratio) have been explored, but they are not standard tools for decision-making in this setting.

3) Treatment selection

For localized disease, surgery and radiation remain the pillars. Biomarkers inform nuance rather than wholesale changes. For recurrent or metastatic disease, biomarkers can directly influence the systemic options on the table:

• PD-L1 CPS helps select patients for checkpoint inhibitors, either alone or with chemotherapy, per guideline-based criteria.⁸
• MSI-high or deficient MMR status, while rare, supports the use of immunotherapy across tumor types.
• NTRK gene fusions, though uncommon, open a path to TRK inhibitors under tumor-agnostic approvals.¹⁰

One practical example: Two patients with metastatic oropharyngeal cancer might look identical on a scan. If one has a CPS of 20 and the other has a CPS of 0, the immunotherapy discussion will unfold differently. The biomarker does not guarantee outcome, but it sharpens the risk–benefit conversation.

4) Surveillance

After curative-intent therapy, surveillance is mostly clinical examination and symptom-guided imaging. Biomarkers add specificity in two notable scenarios:

• HPV-positive oropharyngeal cancer: HPV ctDNA can detect molecular recurrence earlier. A rising signal may prompt earlier imaging or biopsy.¹²
• Nasopharyngeal carcinoma: Plasma EBV DNA can be monitored at defined intervals. A re-emergent or rising level after being undetectable often triggers workup.

For oral cavity and lip cancers without viral drivers, there is no validated blood biomarker for routine surveillance. Here, high-quality exams, dental and speech–swallow follow-up, and targeted imaging do the heavy lifting.

Site-by-site biomarker landscape

Lip and oral cavity

These cancers are largely linked to tobacco, alcohol, and in some regions betel nut. UV exposure is a risk driver for lower lip lesions. The key biomarkers are pathologic, not viral or serum based. Margin status, depth of invasion, perineural and lymphovascular invasion,¹⁴ and nodal extranodal extension are the parameters most predictive of outcomes. Genomic profiling rarely yields an immediately actionable target, though it can identify rare fusions or MSI in exceptional cases. Routine blood tumor markers are not recommended.

Oropharynx

HPV/p16 status is central. Add PD-L1 CPS in recurrent/metastatic disease. Consider HPV ctDNA for surveillance in centers that offer it. Comprehensive genomic testing may be useful for clinical trial matching or to discover rare targetable alterations.

Nasopharynx

Plasma EBV DNA is the signature biomarker.⁶ PD-L1 can inform immunotherapy decision-making in advanced disease. Genomic tests can add MSI/TMB context and rare fusions. Salivary EBV markers and antibody panels are studied in endemic regions, but plasma EBV DNA plus imaging and endoscopy remains the practical backbone.

Quality, limitations, and "gotchas" that matter

• Fixation and tissue handling. Over- or under-fixation can affect p16 and PD-L1 staining. Decalcification can damage nucleic acids for HPV or NGS tests.
• Heterogeneity. A small biopsy may miss areas with different PD-L1 expression or genetic alterations. Sometimes a repeat sample is more informative after treatment.
• Assay variability. PD-L1 CPS requires specific antibody clones and scoring rules. TMB cutoffs are lab-specific. EBV DNA assays differ in calibration and units. Results are not always interchangeable across labs.
• Timing. PD-L1 and ctDNA levels can shift with therapy. Comparing like with like is crucial when making decisions based on trends.

If you're comparing reports from different hospitals, look for the exact method name and unit of measure. That's the biomarker equivalent of checking that two bathroom scales are zeroed the same way before comparing weights.

Common questions, answered plainly

Is there a blood test to screen for oral cancer?

No, not at this time. Dentists and clinicians find most early oral cavity cancers through careful exam and attention to persistent sores, white or red patches, or lumps. Salivary and blood panels are being studied but are not validated for general screening.

If my tumor is p16-positive, does that mean I definitely have HPV?

Strong, diffuse p16 staining is a reliable surrogate for transcriptionally active HPV in oropharyngeal cancers. Outside the oropharynx, p16 does not carry the same meaning. When needed, pathologists can add HPV DNA or RNA tests to confirm.

Can PD-L1 score change over time?

Yes. PD-L1 is an adaptive signal that can rise or fall with inflammation, radiation, or systemic therapy. That's one reason PD-L1 is usually measured near the time of treatment decisions in advanced disease.

Does a high PD-L1 guarantee that immunotherapy will work?

No. It increases the odds but does not guarantee benefit. Some low PD-L1 tumors respond, and some high PD-L1 tumors do not. That's why PD-L1 is one factor among many in shared decision-making.

Is EBV DNA ever used for people without nasopharyngeal cancer?

Not routinely. EBV DNA has a specific role in nasopharyngeal carcinoma. Outside that context, elevations usually reflect viral reactivation rather than cancer.

Mechanisms in everyday language

These biomarkers aren't magic; they're biology you can visualize:

• HPV/p16: Think of HPV's E6/E7 proteins as a hacker disabling your phone's security. The phone ramps up an internal alarm (p16). Measuring that alarm tells us the hack is active.
• EBV DNA: Tumors tied to EBV shed tiny fragments of viral DNA into blood. It's like glitter on a craft table. Even after you clean, a little glitter tells you where the action was and whether it's back.
• PD-L1 CPS: Tumors cloak themselves by displaying a "do not attack" flag to immune cells. The CPS quantifies how many flags are present relative to the number of tumor cells.
• MSI/TMB: When the spell-checker for DNA is broken, typos pile up. Those typos create novel protein snippets that the immune system can recognize, making immunotherapy more effective.

Life stage, sex, and population differences that are real

HPV-positive oropharyngeal cancer more commonly affects middle-aged men, often without heavy smoking histories. Nasopharyngeal carcinoma is more frequent in parts of East and Southeast Asia, North Africa, and among certain diaspora populations, reflecting genetic and environmental factors. These patterns influence which biomarkers are prioritized. In pregnancy, diagnostic pathways emphasize imaging and procedures that minimize fetal exposure, but the biomarker playbook itself does not change materially. Pediatric cases are rare and typically managed at specialized centers where biomarker testing follows similar principles but with age-specific expertise.

How results can change the plan: realistic scenarios

Here are concrete, guideline-aligned ways biomarker results shape care without prescribing specific treatments:

• An oropharyngeal tumor is p16-positive. The stage grouping shifts, the prognosis improves, and the team may consider protocols that aim to preserve swallowing and speech while maintaining cure rates.⁴
• A nasopharyngeal cancer has high baseline EBV DNA that drops to undetectable after therapy. Follow-up can use EBV DNA as a personalized barometer, alongside exam and imaging.
• A recurrent tumor has PD-L1 CPS of 20. The immunotherapy discussion becomes more favorable based on trial data and guideline criteria for recurrent/metastatic disease.
• NGS reveals an NTRK fusion. The patient becomes eligible for a tumor-agnostic targeted therapy, often via a specialty access pathway.
• MSI-high status is discovered in an otherwise typical oral cavity cancer. This opens immunotherapy options and can prompt genetic counseling because mismatch repair defects sometimes signal heritable syndromes.

What to look for in your lab report

You don't need to speak lab shorthand to spot the essentials. These anchors matter:

• Exact test and method. For PD-L1, look for "CPS" and the antibody clone. For HPV, is it p16 IHC alone or combined with HPV DNA/RNA testing. For EBV, confirm plasma DNA by quantitative PCR and units.
• Cutoffs and interpretation. Reports should state thresholds (e.g., CPS ≥1) and a brief interpretive comment tied to clinical use.
• Specimen adequacy. Tiny biopsies or decalcified samples can limit certain tests. If limited, the report should say so.
• Trends over time. For EBV DNA and HPV ctDNA, a graph of values over visits tells the story better than a single number.

Practical limitations and responsible caveats

Biomarkers do not replace a full clinical picture. A low PD-L1 does not close the door on immunotherapy. A negative ctDNA does not exclude microscopic disease. A positive p16 outside the oropharynx can be misleading. Assay differences across labs can change numeric values without reflecting true biologic change. And insurance coverage often follows guideline indications, which can affect when and how tests are ordered. These realities are not flaws; they are the reason results are interpreted in context by a multidisciplinary team.

Where the field is heading

Three areas are moving fast:

• De-escalation strategies for HPV-positive oropharyngeal cancer that use molecular response (like clearance of HPV ctDNA) to tailor intensity, aiming to protect long-term swallowing, taste, and dental health while maintaining cure rates.¹⁵
• Standardization of EBV DNA testing globally to harmonize units and cutoffs so results are more comparable across centers.⁶
• Salivary and blood-based early detection panels, particularly methylation signatures, that may someday complement clinical exams. These are promising but require rigorous validation.

Expect incremental change rather than overnight revolutions. Big studies and careful follow-up protect patients from hype and ensure that what "works" in a paper actually helps in real clinics.

Bottom line

Biomarkers in lip, oral cavity, and pharyngeal cancers are not abstract science. They are practical tools that make care more precise. For oropharyngeal cancers, p16/HPV status reshapes staging and prognosis. For nasopharyngeal cancers, plasma EBV DNA functions as a sensitive, real-time tracker. In advanced disease, PD-L1, MSI, TMB, and rare fusions help align therapies with tumor biology. Liquid biopsies, especially EBV DNA and HPV ctDNA, add an early warning system for select patients. Every result lives in context. The strongest outcomes happen when biomarker data, imaging, pathology, and the lived experience of the person in front of us all inform one plan.