Essential Guide to Biomarkers for Lung, Bronchus, and Trachea Cancers

If lung cancer is the headline you never wanted to see, biomarkers are the plot twist that can change the story. A biomarker is a measurable sign of what's happening inside a tumor, from the DNA driving its growth to proteins that tell your immune system whether to attack. In cancers of the lung, bronchus, and trachea, biomarkers help confirm the diagnosis, choose targeted therapies, tune immunotherapy, and track response over time.¹

This guide translates the science into plain language so you can understand what tests are used, why they matter, and how to interpret results with your care team.

The airway cancer landscape: what we're talking about

Most cancers found in the chest airways start in the lungs, specifically the bronchial tree that branches through the lung. "Tracheal cancer" is rare but managed by many of the same teams and, in some cases, with the same tests. The big buckets are:

• Non-small cell lung cancer (NSCLC): includes adenocarcinoma, squamous cell carcinoma, and large-cell carcinoma
• Small cell lung cancer (SCLC): a fast-growing neuroendocrine cancer strongly linked to smoking
• Rare primary tracheal tumors: often squamous cell carcinoma or adenoid cystic carcinoma

Biomarkers are most deeply developed for NSCLC. SCLC and rare tracheal tumors also have useful markers, though the playbook differs.

How biomarker testing actually happens

Most biomarker testing starts with tumor tissue. That can be a needle biopsy guided by CT or ultrasound, a bronchoscopic biopsy, or sometimes a bit of lymph node sampled during staging.

Pathologists first confirm the cancer type under the microscope. Then the lab runs molecular and protein tests. The exact order varies by center, but a modern, guideline-based approach reflexes to a broad DNA/RNA panel so you don't lose time testing one gene at a time. If tissue is scarce, labs can test tumor DNA floating in the blood (circulating tumor DNA, or ctDNA). A negative blood test doesn't rule out a mutation — it may simply mean the tumor isn't shedding enough DNA into the bloodstream.

Assays you may see on a report include:

• NGS (next-generation sequencing): reads many genes at once to find mutations, fusions, and copy changes
• IHC (immunohistochemistry): stains for proteins like PD-L1 or neuroendocrine markers
• FISH (fluorescence in situ hybridization) or RNA-based methods: help confirm gene fusions (ALK, ROS1, RET, NTRK)
• Liquid biopsy: NGS on blood to detect tumor DNA and track treatment response

Why biomarkers change treatment choices

Two big categories dominate in lung cancer care:

• Predictive biomarkers: forecast whether a therapy is likely to work (e.g., EGFR mutation predicts benefit from an EGFR inhibitor)
• Prognostic biomarkers: foretell the cancer's behavior regardless of treatment (e.g., stage or certain co-mutations)

Think of predictive biomarkers as "matching the key to the lock." When the key fits, targeted therapy can sometimes shrink tumors rapidly, even when they're advanced. Immunotherapy relies on different markers, most famously PD-L1, to estimate how primed the tumor microenvironment is for an immune response.

The must-know actionable biomarkers in NSCLC

For adenocarcinoma and other non-squamous NSCLC — and in any never-smoker regardless of histology — guidelines recommend testing a full panel of oncogenic drivers. Squamous cell cancers can also harbor these changes, especially in never-smokers or small biopsies where the subtype isn't crystal clear.

EGFR (epidermal growth factor receptor)

What it is: Mutations in EGFR act like a jammed accelerator, keeping growth signals on. Common sensitizing mutations include exon 19 deletions and L858R. Less common variants (exon 20 insertions, G719X, L861Q, S768I) have varied sensitivity profiles.²

Who it's seen in: More common in never-smokers, women, and people of East Asian ancestry, but it appears across all groups.²

Why it matters: EGFR-mutant NSCLC is often highly responsive to EGFR inhibitors. Resistance can emerge over time through secondary mutations or signaling "workarounds," which is why re-testing at progression is useful.³

ALK rearrangements

What it is: A gene fusion rewires ALK to be abnormally active.⁴

Who it's seen in: Typically younger patients and never- or light-smokers with adenocarcinoma.

Why it matters: ALK inhibitors can produce deep, durable responses, including activity in brain metastases for some agents. Resistance often arises through ALK mutations or bypass tracks — repeat profiling can guide the next move.

ROS1 rearrangements

What it is: Another fusion event activating ROS1.

Who it's seen in: Often never-smokers with adenocarcinoma.

Why it matters: ROS1 inhibitors are effective; testing is best done with NGS including RNA or with validated FISH.⁵

MET exon 14 skipping

What it is: A splice alteration that prevents normal degradation of MET, leading to persistent signaling.⁵

Why it matters: MET inhibitors can be effective. Since this is a splicing change, RNA-based assays often catch it more reliably than DNA-only tests.

RET and NTRK fusions

What they are: Gene fusions creating abnormal signaling proteins.⁵

Why they matter: Potent, selective inhibitors exist. Fusions are best detected with RNA-based NGS to avoid false negatives.

BRAF V600E

What it is: A specific point mutation flipping BRAF into the "on" position.

Why it matters: Combined pathway inhibition can be effective for this mutation.

KRAS (with focus on G12C)

What it is: KRAS mutations are the most common driver in Western populations. G12C is linked to prior tobacco exposure.⁶

Why it matters: KRAS G12C inhibitors are available, and co-mutations (like STK11 or KEAP1) can influence behavior and immunotherapy response in complex ways.⁶ KRAS mutations can impair tumor-infiltrating T cell function and create an immunosuppressive tumor microenvironment, making combination therapies with immunotherapy particularly appealing.⁷

ERBB2/HER2

What it is: ERBB2 alterations include exon 20 insertions and amplification.

Why it matters: Targeting HER2 alterations has shown benefit in lung cancer, though the specific alteration type guides expectation.

A practical note: Different alterations call for different detection techniques. Fusions benefit from RNA assays; copy number changes may need confirmation; exon 20 insertions can be missed by older PCR panels. Comprehensive NGS improves the odds of getting a complete picture in one pass.

Immunotherapy markers: PD-L1, TMB, and MSI

PD-L1 by IHC

PD-L1 is a protein some tumors use to turn off T-cells. Pathologists report a Tumor Proportion Score (TPS) as a percentage. Higher PD-L1 generally correlates with greater chance of benefit from immune checkpoint inhibitors.⁸ A TPS of 50% or more is often considered "high." That said, some low-PD-L1 tumors still respond, and some high-PD-L1 tumors don't — biology is messy.

Assay nuance: Several PD-L1 antibody clones and platforms exist (e.g., 22C3, SP263). They are similar but not identical, so your report will specify which assay was used. Minor differences can shift the percentage near a cutoff.

Tumor mutational burden (TMB)

TMB estimates how many mutations are present across the tumor genome. Smoking-related tumors typically have higher TMB, which can create more "foreign" signals for the immune system to see.⁹ Studies suggest TMB-high status may predict better responses to immunotherapy, though cutoffs and measurement methods vary across labs. It's a helpful context marker rather than a solo decision-maker.

Microsatellite instability (MSI) and mismatch repair (MMR)

MSI-high is rare in lung cancer but important when present. MSI-high tumors often respond well to immunotherapy across cancer types.⁹ If your NGS report flags MSI-high or MMR deficiency, clinicians pay attention.

Serum tumor markers: helpful in context, not for screening

Blood-based tumor markers are appealing because they're easy to draw. In lung cancers, they can help with monitoring, especially in neuroendocrine tumors, but they're not recommended for screening or for making a diagnosis on their own.

• CEA: may rise in adenocarcinoma; also elevated in smokers and benign conditions
• CYFRA 21-1: associated with squamous cell carcinoma; can rise with kidney disease
• SCC antigen: squamous-associated; can be elevated in non-cancer conditions
• NSE and ProGRP: used more in SCLC and other neuroendocrine tumors; NSE is falsely high with hemolysis

When used, these markers serve as trends to complement imaging. A single value rarely answers a clinical question without context.

Small cell lung cancer: different biology, evolving markers

SCLC behaves differently from NSCLC — it grows quickly, responds briskly to chemotherapy, and often relapses. Classic neuroendocrine markers (synaptophysin, chromogranin, INSM1) define the phenotype under the microscope. Blood markers like ProGRP and NSE can help follow disease activity.¹⁰

PD-L1 is less predictive in SCLC compared with NSCLC. A newer marker, DLL3, is expressed on many SCLC cells and is being used to select patients for emerging therapies.¹¹ This area is moving fast; ongoing trials continue to refine who benefits most.

Tracheal and bronchial primaries: rare but not invisible

Primary tracheal cancers are uncommon. Two patterns matter for biomarkers:

• Squamous cell carcinoma of the trachea: overlaps biologically with lung squamous cancers; PD-L1 testing can inform immunotherapy considerations
• Adenoid cystic carcinoma (ACC): often harbors MYB or MYBL1 rearrangements and can express c-KIT; molecular confirmation supports the diagnosis and clinical trials

Mucoepidermoid carcinoma of the bronchus is another rare entity, sometimes featuring a CRTC1-MAML2 fusion. These tumors behave differently from typical NSCLC, which is why getting the diagnosis right is the first "biomarker" decision.

Liquid biopsy: when blood can stand in for tissue

Liquid biopsy looks for tumor DNA fragments in blood. It can identify targetable mutations, detect resistance changes, and track response between scans.¹² In newly diagnosed advanced NSCLC, a positive liquid biopsy can accelerate treatment decisions while waiting for tissue results. A negative liquid biopsy, however, doesn't mean "no mutations" — it can simply reflect low tumor DNA shedding. Tissue testing remains the reference standard, especially for gene fusions and when results will steer first-line decisions.

Limitations to know:

• Clonal hematopoiesis: age-related mutations in blood cells can mimic tumor mutations; experienced labs filter these out, but rarities occur
• Low-shedding tumors: early-stage disease, purely intrathoracic tumors, or treated disease may yield false negatives
• Assay differences: panels vary in gene content, depth, and bioinformatics; results from different vendors aren't always apples-to-apples

Minimal residual disease (MRD) and response monitoring

MRD testing uses highly sensitive, often "tumor-informed" assays to look for tiny amounts of cancer DNA after surgery or chemoradiation. In research and select clinical settings, ctDNA clearance after treatment predicts better outcomes and ctDNA reappearance can foreshadow relapse months before imaging.¹³ This is an exciting frontier, but it's not yet a universal standard for lung cancer — decisions still rely on clinical context and imaging.

Resistance happens: why re-testing matters

Targeted therapies work until the tumor finds a workaround. Examples include second-site mutations in EGFR or ALK, amplification of MET, brand-new fusions, or even a change in personality where an adenocarcinoma transforms into a small cell–like tumor. When cancer grows after a good response, your team may repeat a biopsy to see what changed. Liquid biopsy can sometimes capture these resistance mechanisms if a tissue procedure isn't feasible.¹⁴

Quality and logistics: what influences a "good" result

Cancer testing is a team sport among interventionalists, pathologists, and molecular labs. A few behind-the-scenes details affect accuracy:

• Tumor content: pathologists estimate the percentage of tumor cells; very low tumor content can dilute mutations
• Fixation and processing: certain decalcifying agents damage DNA; proper formalin fixation preserves it
• RNA vs DNA: fusions and splicing changes are better caught with RNA-based methods
• Assay breadth: comprehensive panels reduce the risk of missing a rare but actionable alteration
• Turnaround time: PD-L1 often returns in days; full NGS can take 1 to 3 weeks

If a report seems incomplete, it's reasonable for clinicians to ask the lab about sample adequacy, coverage of key genes, and whether a complementary RNA fusion panel or repeat sampling would add clarity.

Risk, exposures, and what biomarkers do (and don't) tell you

Smoking drives many of the DNA changes we see in lung cancer. That's one reason smokers tend to have higher TMB, which can affect immunotherapy discussions. Radon exposure in homes and certain workplaces, asbestos, and air pollution also contribute risk. Biomarkers reflect the tumor you have; they don't measure past exposure directly. If you're picturing that one viral supplement solving this — that's not how biology works. Risk changes slowly, and medical decisions hinge on the tumor's current molecular profile, not on a single blood vitamin level.

Special situations worth knowing

• Never-smokers with lung adenocarcinoma: higher chance of an actionable driver like EGFR, ALK, ROS1, or RET
• Women and East Asian ancestry: increased prevalence of EGFR mutations²
• Brain or leptomeningeal spread: some targeted agents penetrate the central nervous system; in rare cases, cerebrospinal fluid ctDNA helps with detection when standard biopsies aren't possible
• Pleural effusions: cell blocks made from fluid can be excellent for PD-L1 and NGS if enough tumor cells are present

Putting results in context: how clinicians interpret them

Biomarker results don't live in a vacuum. Your team cross-references them with stage, imaging, prior treatments, and overall health. A few examples of how results are integrated:

• High PD-L1 without a targetable driver: immunotherapy may be prioritized
• Actionable driver mutation: targeted therapy typically leads, regardless of PD-L1 level
• Co-mutations: STK11 or KEAP1 may signal tougher biology, steering toward combinations and closer monitoring
• Rising ctDNA with stable scans: prompts careful follow-up; not a solo reason to change therapy in most settings

Studies from large consortia and real-world datasets consistently show that matching therapy to a validated driver improves outcomes. Guideline groups such as NCCN and ESMO recommend broad upfront molecular testing in advanced non-squamous NSCLC and in selected squamous cases. That's because missing a targetable alteration can close doors you want open.

Common questions, answered clearly

Is PD-L1 the only immunotherapy test? No. PD-L1 is the most used, but TMB and MSI can provide added context. Still, PD-L1 remains the primary IHC marker in lung cancer.

Are blood-only early detection tests ready to replace CT scans? Not at this time. Low-dose CT is the proven screening tool for high-risk individuals, reducing lung cancer deaths in randomized trials. Blood-based multicancer tests are promising but not endorsed as a screening replacement for lung cancer.

What if my biopsy is too small to test everything? Labs often triage tissue to prioritize the highest-yield tests. Liquid biopsy can fill gaps. Sometimes a repeat biopsy is worth it to unlock crucial information.

Do results differ across labs? Methodologies and cutoff thresholds can differ, particularly for TMB and PD-L1. Using accredited labs and sticking with one platform when monitoring trends helps minimize noise.

Key takeaways you can use

• Ask whether comprehensive DNA and RNA testing has been done, including fusions and MET exon 14 skipping
• Confirm that PD-L1 was tested and note the percentage and assay used
• If treatment stops working, discuss re-biopsy or liquid biopsy to look for resistance mechanisms
• Use serum tumor markers only as trend tools alongside imaging, not as stand-alone answers
• Keep reports together; your care team benefits from seeing the full testing timeline

Short glossary of terms on your report

• Driver mutation: a genetic change that actively fuels tumor growth
• Fusion/rearrangement: two genes break and rejoin, creating an abnormal signal
• Amplification: extra copies of a gene, often increasing its effect
• PD-L1 TPS: percentage of tumor cells staining positive for PD-L1
• TMB: number of mutations per megabase of DNA sequenced

Credibility cues and caveats

The bottom line

Biomarkers turn a generic cancer label into a personalized map. In lung, bronchus, and trachea cancers, that map guides targeted therapy, tunes immunotherapy, and tracks response in ways that weren't possible a decade ago. The right test, on the right tissue, read in the right context, can widen options and sharpen decisions. Bring your questions and your reports to clinic. The science is complex, but your care should feel clear.