TFEB-altered renal cell carcinomas

• A molecularly defined group of renal carcinomas with TFEB rearrangement or amplification.
• TFEB (6p21.1) is a MiT family transcription factor regulating lysosomal biogenesis, autophagy, metabolism and melanocytic genes.
• TFEB-rearranged RCC: fusion-driven, classically MALAT1::TFEB; younger patients, often biphasic, usually indolent.
• TFEB-amplified RCC: increased copy number, often a broader 6p21 amplicon; older adults, high grade, substantially more aggressive.
• Both can express melanocytic markers and overlap with conventional and eosinophilic RCCs.
• No single morphologic or IHC feature is specific: molecular confirmation is essential.

Diagnostic pearl: rearranged and amplified tumours share a WHO heading but are not clinically interchangeable.

• Age: children and young adults (also older) vs predominantly older adults.
• Alteration: gene fusion vs copy-number amplification.
• Morphology: biphasic, pseudorosettes, nests vs solid, tubular, papillary, pseudopapillary, high grade.
• Nuclei: often relatively bland vs frequently pleomorphic with prominent nucleoli.
• Cathepsin K: usually positive vs variable.
• Melanocytic markers: frequently positive vs variable.
• TFEB IHC: often strong nuclear vs variable.
• Behaviour: usually indolent vs frequently aggressive.
• Main challenge: RCC/PEComa overlap vs separating true amplification from copy-number gain.

These are tendencies: aggressive rearranged and relatively indolent amplified tumours exist.

Biphasic architecture

• Large polygonal cells with clear to eosinophilic cytoplasm in nests, sheets or alveoli; round nuclei, small to moderate nucleoli.
• Small epithelioid cells around rounded deposits of hyaline, eosinophilic basement membrane-like material, forming Call-Exner-like pseudorosettes; may be focal or inconspicuous.

Stroma

• Delicate fibrovascular septa; hyaline deposits are diagnostically useful; peripheral entrapped native tubules are common.

Diagnostic pearl: the biphasic pattern is a powerful clue, but it is absent or limited in a substantial subset.

• Nested / alveolar: mimics ccRCC or TFE3-rearranged RCC.
• Solid: small cells inconspicuous; differential widens to oncocytic RCC, epithelioid AML and other MiT tumours.
• Papillary / pseudopapillary: mimics TFE3-rearranged RCC or PRCC.
• Tubular / tubulocystic: may lack biphasic features.
• Oncocytic: granular eosinophilic cells mimic oncocytoma or eosinophilic ChRCC.
• Sclerosing / hyalinised: small cells around hyaline spheres become conspicuous.
• Clear cell phenotype: mimics ccRCC, usually without box-like CAIX.
• High grade: rare; marked atypia, necrosis or atypical mitoses warrant evaluation for amplification or additional alterations.
• Entrapped peripheral tubules are not destructive invasion.

Diagnostic pearl: absent pseudorosettes do not exclude TFEB rearrangement; sample extensively and confirm molecularly.

• PAX8: frequently positive; key when keratins are absent and melanocytic markers strong.
• TFEB: nuclear; useful screen, not proof of rearrangement (fixation and protocol dependent).
• Cathepsin K: usually strong; not specific (EVT, ESC RCC, PEComa).
• HMB45, Melan-A: frequently positive, may be heterogeneous.
• Pancytokeratin / EMA: variable, often focal or negative.
• CK7: usually negative or limited.

Diagnostic pearl: PAX8+ with TFEB, cathepsin K and melanocytic markers strongly suggests TFEB-rearranged RCC, but molecular evidence remains necessary.

MALAT1::TFEB

• t(6;11)(p21;q12); MALAT1 (formerly Alpha) is a noncoding RNA gene.
• Places intact TFEB under strong regulatory elements: overexpression, not a chimeric oncoprotein.

Alternative partners

• ACTB, NEAT1, COL21A1, CADM2, EWSR1, CLTC, PPP1R10, KHDRBS2: some known only from single cases.

Testing

• Unusual partners can give nonclassic morphology; cryptic rearrangements may escape break-apart FISH, so RNA fusion testing can be decisive.

Behaviour

• Mostly indolent after resection, lower stage than amplified tumours; recurrence and metastasis uncommon but documented (necrosis linked to adverse behaviour).
• Recent series of 14: 8 biphasic; partners MALAT1 (5) and ACTB (1); no recurrence or metastasis over 3–122 months.

• Increased copy number of 6p21.1, often with VEGFA and CCND3 in the amplicon.
• Older adults; high-grade nuclei; heterogeneous architecture; biphasic pseudorosettes generally absent.
• Cathepsin K and melanocytic markers less consistent than in rearranged tumours.
• No universally validated amplification threshold.
• Often advanced stage; metastasis and tumour death common in reported cohorts.

Histology

• Mostly solid, with pseudopapillary, tubular, nested, alveolar or papillary areas; may resemble high-grade ccRCC or PRCC.
• Large cells with abundant eosinophilic granular or amphophilic cytoplasm; clearing or vacuoles possible.
• Enlarged pleomorphic nuclei, prominent nucleoli, mitoses, necrosis; rhabdoid or sarcomatoid areas; vascular invasion.
• Some tumours contain bland oncocytic areas that mislead on biopsy.

Diagnostic pearl: TFEB-amplified RCC is not a high-grade variant of the rearranged tumour; it is genomically and clinically distinct.

• Dense granular eosinophilic cytoplasm, usually without the coarse basophilic stippling of ESC RCC.
• Focal vacuoles: overlap with EVT; nonspecific.
• Extracellular magenta globules between cells or in lumina: useful, not exclusive.
• Apical nuclei in pseudopapillary and tubular areas can mimic CCPRCT polarisation; high-grade nuclei help.
• Calcifications: nonspecific.
• Mixed clear and eosinophilic cells in the same tumour are common.

Diagnostic pearl: dense eosinophilic cytoplasm + pseudopapillary/loose tubules + high-grade nuclei + magenta globules is suggestive; confirm molecularly.

• PAX8: usually positive.
• TFEB: variable nuclear; a negative stain does not exclude amplification, and non-amplified tumours may stain.
• Cathepsin K: variable, often focal or negative; negative does not exclude.
• HMB45 / Melan-A: variable, frequently incomplete.
• CK20: sometimes positive, so CK20 does not prove ESC RCC.
• CK7: usually negative or focal; AMACR frequently positive.
• PD-L1: frequent membranous expression in selected cohorts; not a validated predictor.

Diagnostic pearl: a PAX8+ RCC with an unusual eosinophilic phenotype may need TFEB copy-number testing even when TFEB and cathepsin K stains are negative.

• High-level amplification: clustered FISH signals or marked focal copy-number elevation.
• Amplicon may include VEGFA (angiogenic rationale, not a predictor for an individual tumour) and CCND3 (cell cycle; prognostic value uncertain), depending on its boundaries.
• High-level focal amplification is more convincing evidence of a driver than broad chromosome 6 gain or polysomy.
• Low-level increases are an interpretive grey zone.

Diagnostic pearl: the focality, magnitude and relationship to chromosome 6 dosage matter more than the absolute TFEB signal count.

No universally accepted or prospectively validated threshold exists.

Proposed FISH categories (AJSP 2025)

• 2 signals: diploid. 3–4: increased copy number, below threshold.
• 5–10: low-level amplification. >10: high-level amplification.
• Proposed practical threshold ≥5 copies; 15 amplified tumours (5 high, 10 low level); validation needed. Not WHO criteria.
• CNV analysis showed a specific 6p21.1 amplicon in 1 high- and 2 low-level tumours, but none in 4 tumours with 3–4 signals.

Why absolute counts mislead

• Chromosome 6 polysomy raises TFEB and reference signals together.
• Low-level gain vs true amplification are biologically different.
• Heterogeneity: biopsies may miss high-level areas; averages hide subclones.
• Platforms: FISH and NGS copy numbers are not interchangeable (purity, ploidy, normalisation).
• Prognosis: no validated copy-number boundary predicts outcome.

Report

• Signal number and distribution, proportion of nuclei, focal vs chromosome 6 gain, TFEB/reference relationship, clustering, assay and cutoff used, NGS confirmation.

Diagnostic pearl: “five TFEB copies” is a proposed operational threshold, not an established boundary; describe uncertain copy-number changes rather than labelling them amplified.

Rearrangement plus amplification

• Both can coexist (3 such tumours in the recent AJSP amplified group); significance uncertain.
• A positive break-apart FISH does not exclude accompanying amplification; report each mechanism.

Break-apart FISH

• Partner-agnostic and FFPE-friendly, but does not name the partner; may miss cryptic intrachromosomal events; extra signals may be gain or amplification.

RNA sequencing

• Names the partner and detects cryptic fusions; depends on RNA quality; does not measure copy number.

DNA copy-number profiling

• Shows focal amplification, VEGFA/CCND3 and chromosome 6 context; affected by purity, ploidy and platform thresholds.

Diagnostic pearl: decide whether the copy-number change is focal and disproportionate to chromosome 6, not just how many signals there are.

Epithelioid angiomyolipoma

• Both: large epithelioid eosinophilic cells, solid or nested growth, melanocytic markers, cathepsin K.
• TFEB RCC: PAX8 often positive, keratin/EMA variable, TFEB alteration. EAML: PAX8 and keratin negative, TSC1/TSC2 altered; thick vessels or fat if present.
• HMB45/Melan-A should not by themselves classify a renal tumour as EAML; TFE3-rearranged PEComa is another differential.

ESC RCC (Zullow, Histopathology 2026: 9 ESC vs 6 TFEB-amplified)

• ESC: solid-cystic, tightly packed small tubules, coarse stippling, hobnail cysts, macrophages, TSC1/TSC2.
• TFEB-amplified: solid, pseudopapillary, loose tubules, dense granular cytoplasm, apical nuclei, magenta globules.
• CK20+ in 7/9 vs 3/6; Melan-A+ in 2/9 vs 4/6; differences not significant.

Diagnostic pearl: neither CK20 positivity nor Melan-A negativity reliably separates ESC RCC from TFEB-amplified RCC.

• TFE3-rearranged RCC: nested, papillary or solid; may be biphasic; cathepsin K and melanocytic overlap; TFE3 and TFEB stains are not interchangeable; use gene-specific FISH or RNA-seq.
• Clear cell RCC: capillary network, box-like CAIX, VHL/3p loss; clear cell-rich TFEB tumours need molecular exclusion.
• Papillary RCC: CK7/AMACR overlap; discordant high-grade eosinophilic papillary tumours deserve TFEB testing.
• EVT: large vacuoles, thick-walled vessels, CD117+, TSC/MTOR; amplified RCC may contain vacuolated cells.
• FLCN-associated tumours: TFEB pathway markers without a TFEB alteration; BHD context.
• Metastatic melanoma: S100, SOX10; PAX8 and a TFEB fusion favour RCC.

Diagnostic pearl: cathepsin K, HMB45, Melan-A and nuclear TFEB point a direction; they do not define the entity.

1. Suspect: biphasic tumour with pseudorosettes, unusual oncocytic tumour with melanocytic differentiation, or heterogeneous high-grade solid/pseudopapillary carcinoma.
2. Panel: PAX8, broad keratin, cathepsin K, HMB45, Melan-A; TFEB IHC if validated locally.
3. Rearrangement: break-apart FISH or RNA fusion assay; negative FISH does not exclude cryptic events.
4. Copy number: TFEB vs chromosome 6; separate low-level gain, focal and high-level amplification.
5. Reconcile discordance: other subtypes, assay limits, heterogeneity.
6. Report the mechanism: rearranged, amplified or both, with uncertain findings described.

On biopsy

• Biphasic areas and hyaline deposits may be missed; keratin-negative, melanocytic cores can be misread as EAML.
• Bland oncocytic regions of an amplified carcinoma underestimate the tumour; amplification is heterogeneous.
• Wording: RCC with features suspicious for TFEB alteration; molecular confirmation recommended.

Diagnostic pearl: do not call a tumour TFEB-amplified only because a copy number marginally exceeds one study’s threshold.

Rearranged

• Usually lower stage and indolent; metastasis uncommon but established; fusion-specific prognosis unknown.

Amplified

• Older adults, high grade, often locally advanced; metastasis and death well documented; high-level amplification may be more aggressive, but no validated prognostic threshold.

Recent AJSP cohort

• Rearranged: 0/14 recurrence or metastasis. Amplified: 8/13 metastasis, 3 tumour-related deaths. Selected institutional cases, not population risk.

Diagnostic pearl: distinguishing the mechanism has real prognostic consequences.

• Cutoff unsettled: ≥5 copies proposed; 3–4 signal tumours lacked a 6p21.1 amplicon. Open questions: absolute count vs ratio vs focality, low vs high level, polysomy, independence from grade and stage.
• ESC RCC comparison (Zullow 2026) clarified morphologic clues, but overlap keeps molecular testing important.
• PD-L1: membranous in 9/10 rearranged and 11/13 amplified tumours in one cohort; not a validated predictive or diagnostic marker.
• Separate biology: rearranged and amplified tumours differ in mechanism, age, histology and outcome; report and study them separately.
• New tools: RNA-seq for cryptic fusions, NGS copy-number profiling, TRIM63 RNA-ISH and GPNMB as surrogates (also active in mTOR/FLCN tumours).

• Two subgroups: rearranged (young, indolent) and amplified (older, aggressive).
• Classic rearranged: biphasic, small cells around basement membrane-like material; not always present.
• MALAT1::TFEB is canonical; rare partners exist; cryptic fusions may need RNA-seq.
• Rearranged tumours: cathepsin K, HMB45, Melan-A; keratins weak or negative; PAX8 helps against EAML.
• Amplified tumours: solid, pseudopapillary, tubular, high grade; dense eosinophilic cytoplasm and magenta globules.
• Amplified RCC can be CK20+ and mimic ESC RCC.
• TFEB IHC is technically variable; break-apart FISH does not name partners.
• Amplicon may include VEGFA and CCND3.
• No universal amplification cutoff; ≥5 copies is a proposal; separate chromosome 6 polysomy from focal amplification.
• Rearrangement and amplification can coexist; report the mechanism.