NUT Carcinoma

Slide 1 · NUT Carcinoma

A fusion-driven, poorly differentiated malignancy

Molecular pathogenesis · diagnostic pathology · clinicopathologic correlation

Dr Abu Suraih Sakhri

MBBS, MD (Pathology)

www.abusuraihsakhri.com

Slide 2 · Learning outcomes

Recognize clinical and microscopic settings that warrant NUT testing.

Explain how NUTM1 fusion proteins disrupt chromatin regulation and differentiation.

Construct a focused immunohistochemical and molecular diagnostic pathway.

Interpret key management and prognosis limitations.

Slide 3 · NUT carcinoma is molecularly defined

Poorly differentiated carcinoma

NUTM1 fusion

NUT carcinoma

A rare, aggressive carcinoma driven by an oncogenic NUTM1 rearrangement.

The defining alteration is more specific than a site, age, or conventional histologic pattern.

The malignant cells commonly appear poorly differentiated, with variable squamous features.

Slide 4 · Why this entity is underrecognized

The tumor can closely resemble conventional squamous cell carcinoma.

Unusual site and age distributions can obscure the diagnosis.

Morphology alone cannot reliably identify the molecular entity.

Slide 5 · Anatomic distribution is broad

Primary NUT carcinoma

Head and neck

Thorax

Other sites

Head and neck sites include sinonasal tract, nasopharynx, and salivary glands.

Thoracic and mediastinal primary tumors are also well documented.

Other visceral or extranodal sites occur; “midline” is not an absolute restriction.

Slide 6 · Historical “midline carcinoma” is a misnomer

The historical label reflects the first-recognized thoracic and upper aerodigestive cases.

NUTM1-rearranged carcinomas can arise outside the midline.

“NUT carcinoma” is the preferred broad term for this entity.

Slide 7 · There is no age-based exclusion

Clinical assumption

Diagnostic correction

Pediatric-only tumor

May occur across the lifespan

Young adults only

Older patients also affected

Age confirms diagnosis

Molecular or NUT IHC evidence is required

Cases range from infancy to late adulthood.

A young patient with a rapidly growing undifferentiated carcinoma warrants heightened suspicion.

Advanced age does not exclude NUT carcinoma.

Slide 8 · True population incidence remains uncertain

Disease rarity and histologic mimicry complicate ascertainment.

Selective use of NUT testing creates underdiagnosis and referral bias.

Published case-series proportions should not be presented as population incidence.

Slide 9 · No established environmental cause

Somatic rearrangement

Fusion oncoprotein

Transformation

No specific exogenous cause of the NUTM1 fusion has been established.

A NUTM1 rearrangement is generally a somatic tumor event, not a hereditary syndrome.

Smoking, EBV, and HPV are not established drivers of this entity.

Slide 10 · Head and neck presentation depends on site

Sinonasal lesions may present with nasal obstruction or epistaxis.

Nasopharyngeal or salivary-region masses can produce compressive symptoms.

These symptoms are nonspecific; Rapid progression should raise diagnostic urgency.

Slide 11 · Thoracic disease can be clinically silent early

Mediastinal or pulmonary masses may cause cough, pain, or dyspnea.

Patients may present with bulky locoregional disease.

Clinical presentation cannot distinguish NUT carcinoma from common lung tumors.

Slide 12 · Aggressive local growth has diagnostic consequences

Rapid tumor growth

Limited or necrotic biopsy

Need planned testing

Rapid expansion may compromise airway or adjacent organs.

Necrosis and crush artifact are frequent challenges in limited biopsies.

Early pathology communication can preserve tissue for molecular work-up.

Slide 13 · Dissemination often occurs early

Regional nodes and distant deposits may be present at diagnosis.

Thoracic and extrathoracic primaries both require appropriate staging assessment.

The presence of metastases does not resolve the differential diagnosis.

Slide 14 · Biopsy strategy: Maximize useful viable tumor

Viable tissue

Broad lineage assessment

NUT ± fusion testing

Select a viable region whenever possible, avoiding exclusively necrotic tissue.

Obtain sufficient material for morphology, immunostains, and potential sequencing.

Discuss differential diagnosis with the sampling team if NUT carcinoma is suspected.

Slide 15 · Histology: Primitive epithelial malignancy

Sheets, nests, or lobules of monotonous poorly differentiated cells are common.

Architectural differentiation may be minimal or absent.

Cellular morphology often resembles basaloid squamous carcinoma.

Slide 16 · The nuclear appearance can be deceptively uniform

Observation

Interpretation

Monotonous cells

Primitive appearance

Prominent nucleoli

High-grade cytology

Limited pleomorphism

Does not imply low-grade biology

Nuclei may be round to oval, with open chromatin and evident nucleoli.

Pleomorphism may be less striking than expected for an aggressive tumor.

Nuclear monotony is a clue, not a diagnostic criterion.

Slide 17 · High turnover produces necrosis and mitoses

Rapid proliferation

Demand exceeds local supply

Tumor necrosis

Brisk proliferation commonly accompanies extensive viable tumor.

Confluent necrosis may occur within cellular sheets.

A small sample dominated by necrosis may obscure the epithelial pattern.

Slide 18 · Abrupt keratinization is an important clue

Primitive component

Differentiated component

Basaloid cells

Keratinizing squamous nests

Limited cytoplasm

Eosinophilic keratinization

High proliferation

Abrupt morphologic transition

Well-differentiated squamous foci may directly abut primitive cells.

The shift can occur without an extended maturation gradient.

This feature is helpful but neither constant nor specific.

Slide 19 · Absence of keratinization does not exclude NUT

Some tumors lack visible squamous maturation entirely.

Small biopsies may miss an otherwise focal squamous component.

NUT testing must follow the total clinicopathologic impression, not one morphologic sign.

Slide 20 · Stroma and inflammatory cells can vary

Stroma may be fibrous, edematous, or myxoid.

Intratumoral neutrophils are described and may be conspicuous.

Neither stromal pattern nor inflammatory phenotype is independently diagnostic.

Slide 21 · H&E findings are a trigger—not proof

Pattern recognition

NUT protein IHC

Genetic confirmation when needed

Poor differentiation, necrosis, and focal squamous features form a useful pattern.

The same pattern can occur in several unrelated malignancies.

A molecularly specific assay is needed to distinguish the entity.

Slide 22 · Small biopsy pitfalls require a deliberate sequence

Lineage assessment

Focused differential

NUT testing

First establish carcinoma versus lymphoma, melanoma, or other round-cell tumor.

Then assess squamous and neuroendocrine lineage as indicated.

Order NUT IHC early when the tumor remains unusually primitive.

Slide 23 · Squamous lineage is not sufficient to subtype it

Marker class

What it establishes

Broad cytokeratin

Epithelial differentiation

P40 / p63

Squamous differentiation

NUT nuclear staining

Supports NUT carcinoma in context

Cytokeratin, p40, or p63 positivity may support epithelial/squamous differentiation.

Conventional basaloid SCC can share these markers.

Only NUT-specific testing resolves the molecular classification.

Slide 24 · The genetic hallmark is a NUTM1 fusion

Normal chromosomal segments

BRD4 · 19p13

NUTM1 · 15q14

BRD4 :: NUTM1 fusion protein

Schematic: Rearranged chromosome produces a chimeric transcriptional regulator.

Slide 25 · BRD4 is the major fusion partner

Most commonly identified fusion

BRD4::NUTM1

Other partners

Predominant fusion; Approximately 70% in published series

BRD4 lies at chromosome 19p13 and encodes a BET chromatin reader.

BRD4::NUTM1 accounts for the majority of characterized cases.

Partner identification helps explain mechanism and may inform clinical studies.

Slide 26 · Other partners use related chromatin machinery

NUTM1

BRD4 (major)

BRD3

NSD3 / others

BRD3::NUTM1 and NSD3::NUTM1 are established variants.

ZNF-related and other rare NUTM1 partners have been reported.

Not every NUTM1-rearranged neoplasm is classifiable as NUT carcinoma.

Slide 27 · Fusion terminology matters in the report

Laboratory result

Appropriate wording

Diffuse NUT IHC

NUT carcinoma supported

NUTM1 break-apart FISH

NUTM1 rearrangement detected

RNA fusion assay

Named partner::NUTM1 fusion

Use “NUTM1 rearranged” for a demonstrated locus alteration.

Use “BRD4::NUTM1” only when that partner is actually identified.

Do not infer BRD4 solely from positive NUT immunohistochemistry.

Slide 28 · BRD4 reads acetylated chromatin

Acetylated histone

BRD4 bromodomain binding

NUT tethering

BET bromodomains recognize acetylated lysines on histones.

This property anchors BRD4-containing complexes to active chromatin.

In the fusion protein, the chromatin reader is coupled to NUT activity.

Slide 29 · The NUT moiety recruits acetylation machinery

NUT recruits EP300

Local histone acetylation

More fusion binding

The NUT component interacts with EP300, a histone acetyltransferase.

EP300 increases local histone acetylation at bound chromatin.

More acetylation favors further recruitment of BET-containing fusion protein.

Slide 30 · Feed-forward acetylation builds megadomains

BRD4::NUTM1 binds acetylated histone

NUT recruits EP300

More histone acetylation

Feed-forward chromatin acetylation is a mechanism; Not a measured patient-specific pathway.

BRD4::NUTM1 binds acetylated chromatin and recruits EP300.

EP300 acetylates neighboring histones, extending binding sites.

Repeated recruitment produces large hyperacetylated chromatin domains.

Slide 31 · Megadomains reorganize transcription

Megadomain-associated chromatin

Other chromatin regions

Enriched acetylation

Relative hypoacetylation

Fusion-protein enrichment

Reduced fusion occupancy

Oncogenic gene expression

Differentiation programs impaired

Hyperacetylated domains concentrate oncogenic transcriptional activity.

Regions outside these domains may become relatively hypoacetylated.

The combined effect favors proliferation and represses differentiation programs.

Slide 32 · Differentiation arrest is central to oncogenesis

Fusion-driven transcription

Differentiation blockade

Persistent proliferation

The fusion protein helps maintain a primitive proliferative state.

MYC, SOX2, and TP63 are implicated in experimental models.

Molecular and cell-line evidence must not be mistaken for a validated patient-level biomarker.

Slide 33 · Experimental removal of fusion function restores maturation

Experimental perturbation

Observed cell-model effect

Fusion suppression

Differentiation resumes

BET displacement

Growth arrest / differentiation

Clinical treatment

Benefit remains limited / under study

Fusion knockdown can cause growth arrest and squamous differentiation in models.

BET bromodomain blockade can displace fusion complexes from chromatin.

This is compelling target biology, not proof of clinical survival benefit.

Slide 34 · NUT immunohistochemistry is the frontline assay

Suspect on H&E

NUT IHC

Integrate / confirm

NUT IHC is practical on formalin-fixed diagnostic material.

A strong, diffuse nuclear pattern in an appropriate carcinoma is highly informative.

The assay should be interpreted alongside morphology and controls.

Slide 35 · The characteristic NUT pattern is nuclear

Supports NUT carcinoma

Requires caution

Diffuse nuclear staining

Isolated cytoplasmic staining

Speckled intranuclear pattern

Weak focal nuclear signal

Concordant morphology

Poor preservation / artifact

Strong nuclear labeling frequently has a punctate or speckled quality.

Cytoplasmic staining alone should not be accepted as diagnostic.

Evaluate distribution and intensity in viable tumor nuclei.

Slide 36 · IHC interpretation must remain contextual

Diffuse strong nuclear staining is commonly treated as highly specific in carcinoma.

Test characteristics vary by antibody, sample quality, and population.

Equivocal or discordant staining warrants molecular adjudication.

Slide 37 · Epithelial immunophenotype is variable

Broad-spectrum keratins often support carcinoma.

P40 and p63 may be expressed, sometimes incompletely.

Negative or limited squamous markers do not reliably exclude this entity.

Slide 38 · Neuroendocrine marker expression can mislead

Shared observation

Necessary discriminator

Primitive cells

Lineage panel plus NUT

Necrosis / brisk mitoses

Not exclusive to neuroendocrine tumors

Focal neuroendocrine marker

Does not overrule NUTM1 driver

Some NUT carcinomas express individual neuroendocrine markers.

A small-cell–like morphology does not establish small cell neuroendocrine carcinoma.

Combined morphology and NUT testing can prevent misclassification.

Slide 39 · A negative NUT stain is not the end of work-up

Negative / equivocal IHC

Check specimen and controls

Molecular testing if needed

Review whether viable tissue and assay controls were adequate.

Consider rare antigenic variants, fixation issues, and sampling limitations.

With strong suspicion, request NUTM1 rearrangement or fusion testing.

Slide 40 · Break-apart FISH detects locus rearrangement

NUTM1 locus probes

Rearrangement pattern

Partner still unknown

Separate probes flank NUTM1; An abnormal split signal supports rearrangement.

FISH does not routinely identify the fusion partner.

Preanalytical failure or cryptic rearrangements can require alternative testing.

Slide 41 · RNA-based methods can identify the partner

Tumor RNA

Fusion transcript detection

Partner-resolved diagnosis

Targeted RNA sequencing may detect the expressed fusion transcript.

Partner-resolved results distinguish BRD4, BRD3, NSD3, and rare variants.

Analytic success depends on RNA quality and assay design.

Slide 42 · Use an integrated diagnostic algorithm

Poorly differentiated carcinoma

NUT IHC (diffuse strong nuclear?)

Integrate morphology; Confirm molecularly if equivocal

Identify a poorly differentiated carcinoma and characterize lineage.

Use NUT IHC when histology or clinical context is suspicious.

Use NUTM1 FISH / RNA testing if staining is absent, equivocal, or discordant.

Slide 43 · Basaloid SCC is a major morphologic mimic

Basaloid SCC

NUT carcinoma

Often site-related carcinoma

Can arise in multiple organs

Variable squamous differentiation

Variable squamous differentiation

No defining NUTM1 fusion

NUTM1 rearrangement defines entity

Both tumors may show monotonous basaloid cells, necrosis, and squamous markers.

Abrupt keratinization can also occur outside NUT carcinoma.

A diffuse nuclear NUT stain or defining fusion resolves the distinction.

Slide 44 · Small cell carcinoma enters the differential

Crush artifact, necrosis, and primitive round cells can overlap.

High-grade neuroendocrine lineage requires an integrated marker profile.

NUT expression should be assessed when morphology or markers are atypical.

Slide 45 · Olfactory neuroblastoma is site-specific mimic

Olfactory neuroblastoma

NUT carcinoma

Neuroectodermal lesion

Epithelial carcinoma

Fibrillary matrix often present

Sheets / nests of primitive cells

Neuroendocrine markers support

NUTM1 fusion defines

Sinonasal location and small blue cells create overlap.

Olfactory neuroblastoma often has lobules, fibrillary neuropil, and neuroendocrine markers.

NUT carcinoma requires NUT-specific molecular or immunophenotypic evidence.

Slide 46 · Lymphoma and other round-cell neoplasms

Round-cell neoplasm

Exclude alternate lineages

Target NUT if carcinoma likely

Lymphoma may produce diffuse sheets of blue cells without gland formation.

Melanoma and selected sarcomas can also lose obvious lineage morphology.

A limited first-pass lineage panel avoids a false epithelial assumption.

Slide 47 · SWI/SNF-deficient sinonasal carcinoma

SWI/SNF-deficient carcinoma

NUT carcinoma

Loss of SWI/SNF protein

NUT nuclear labeling

SMARCB1 / SMARCA4 alteration

NUTM1 fusion

Overlapping primitive phenotype

Overlapping primitive phenotype

SMARCB1- or SMARCA4-deficient tumors may also be very poorly differentiated.

Loss of INI1 or BRG1 supports a distinct SWI/SNF-deficient category.

Fusion-based classification should not be replaced by appearance alone.

Slide 48 · EBV-associated nasopharyngeal carcinoma

EBV-related nasopharyngeal carcinoma

NUT carcinoma

EBER positivity supports

NUTM1 fusion supports

Common lymphoid background

Variable inflammatory background

Defined EBV association

No established EBV causation

A nasopharyngeal primary may raise EBV-related carcinoma as an alternative.

Nonkeratinizing nasopharyngeal carcinoma often has a lymphocyte-rich background.

EBER in situ hybridization and NUT testing answer different etiologic questions.

Slide 49 · Germ cell tumor staining is a special pitfall

Normal NUT expression occurs in germ cells, and some germ-cell neoplasms can stain.

Weak or focal staining is different from diffuse strong tumor nuclear reactivity.

Morphology, germ-cell lineage markers, and NUTM1 testing settle conflicts.

Slide 50 · Report the diagnosis with test provenance

Report component

Example information

Morphology

Poorly differentiated carcinoma

Diagnostic evidence

Diffuse nuclear NUT positivity

Genetics (if tested)

BRD4::NUTM1 transcript detected

State tumor type and anatomic site, including certainty about origin.

Specify NUT antibody pattern and/or NUTM1 fusion method.

Name the fusion partner only if directly demonstrated.

Slide 51 · Stage assessment is clinical and site dependent

There is no single universal anatomic staging rubric for all NUT carcinoma sites.

Document primary site, local invasion, nodal disease, and distant metastases.

Staging and treatment planning require the appropriate organ-specific multidisciplinary team.

Slide 52 · Prognosis is poor but not uniform

Anatomic site

Extent at diagnosis

Fusion context

Extreme aggressiveness and survival usually shorter than one year.

Selection, stage, site, fusion partner, and treatment patterns affect reported cohorts.

Avoid promising individual outcomes from small retrospective series.

Slide 53 · Site and fusion partner may stratify risk

Prognosis

Primary site

Disease burden

Fusion partner

Retrospective data suggest thoracic primaries often fare worse than nonthoracic disease.

Among nonthoracic tumors, fusion partner may correlate with survival.

These observations are prognostic associations, not validated treatment selection rules.

Slide 54 · Conventional therapy is often insufficient

Surgery, radiation, and systemic therapy are used in multimodal combinations.

Transient initial responses may be followed by early progression.

No regimen has established a reliable disease-wide cure rate.

Slide 55 · Management of potentially resectable disease

Assess resectability

Local / multimodal therapy

Close reassessment

Discuss complete local resection when anatomically feasible.

Radiation and systemic therapy are considered according to site and extent.

Rarity favors consultation with a specialized multidisciplinary team.

Slide 56 · Advanced disease requires a trial-minded approach

Confirm diagnosis

Multidisciplinary plan

Trial / supportive care

Treatment is individualized; Rapid clinical deterioration is possible.

Systemic therapy and local palliation may both be appropriate.

Clinical trials and expert-center referral should be explored early.

Slide 57 · BET inhibitors are mechanism-directed

BET inhibitor

Fusion–chromatin displacement

Differentiation / growth arrest (models)

They compete with acetyl-lysine recognition at BET bromodomains.

This can displace BRD4::NUTM1 from chromatin in experimental models.

Clinical activity has been limited by durability, toxicity, and heterogeneous responses.

Slide 58 · Additional epigenetic strategies remain investigational

Strategy

Current interpretation

HDAC modulation

Preclinical differentiation signal

BET-based combinations

Clinical investigation

Protein degradation approaches

Emerging research

HDAC inhibitors have produced differentiation-related effects in preclinical models.

Combinations and protein degraders are active areas of research.

Experimental rationale does not equate to a licensed or effective routine treatment.

Slide 59 · Evidence limitations affect clinical recommendations

Most published cohorts are retrospective and relatively small.

Therapies, sites, case ascertainment, and fusion types are heterogeneous.

Rare-disease collaborative registries and prospective studies are important.

Slide 60 · Applied case: A rapidly growing sinonasal mass

Clinical scenario (hypothetical)

A young adult has a destructive sinonasal mass and a primitive carcinoma on biopsy.

The cells form sheets with necrosis and a small focus of squamous maturation.

Question: What next diagnostic test most directly addresses NUT carcinoma?

Discussion question: Establish the next test before revealing the answer.

Slide 61 · Case resolution: Immunophenotype and fusion

Suspicious H&E

NUT IHC

Molecular adjudication if needed

Perform NUT immunohistochemistry early rather than relying on p40 alone.

Diffuse strong nuclear staining supports the molecular diagnosis.

If the result is equivocal, evaluate a NUTM1 rearrangement or transcript.

Slide 62 · Applied case: Negative stain, persistent concern

Clinical scenario (hypothetical)

An undifferentiated mediastinal carcinoma remains unexplained after an initial panel.

A technically limited specimen shows negative NUT IHC.

Question: Does this result definitively exclude NUT carcinoma?

Discussion question: Establish the next test before revealing the answer.

Slide 63 · Case resolution: A negative IHC may be provisional

Assess technical validity

Obtain adequate tissue

NUTM1 molecular assay

Check preservation, controls, and viable tumor content.

Re-biopsy or use an alternate block if needed for adequate testing.

If suspicion persists, molecular testing helps settle discordance.

Slide 64 · Diagnostic sign-out checklist

Is the histologic impression a poorly differentiated carcinoma with an adequate differential?

Was diffuse nuclear NUT expression or a NUTM1 rearrangement demonstrated?

Are fusion partner, site, stage, and diagnostic limitations reported accurately?

Slide 65 · Five high-yield conclusions

NUT carcinoma is defined by a NUTM1 fusion rather than a unique H&E pattern.

BRD4::NUTM1 disrupts chromatin regulation and blocks differentiation.

Diffuse nuclear NUT IHC is an efficient initial diagnostic test.

Negative or equivocal IHC with high suspicion warrants molecular testing.

Disease is highly aggressive; Treatment evidence remains limited.

Slide 66 · Selected references

Robbins, Cotran & Kumar. Pathologic Basis of Disease. 11th ed. 2026; Ch 16, p 674.

Moreno V, Saluja K, Pina-Oviedo S. Front Oncol. 2022;12:860830. doi:10.3389/fonc.2022.860830

Zhang Y, et al. The Innovation. 2026;7(1):101068. doi:10.1016/j.xinn.2025.101068

National Cancer Institute. NUT Carcinoma; Childhood NUT Carcinoma Treatment (PDQ).