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TFE3 / Transcription factor E3 · IHC design guide
Design Immunohistochemistry for TFE3
Plan paraffin-section TFE3 IHC around a mainly nuclear tissue pattern (HPA tissue IHC). Glomerular and Leydig cells show high staining (HPA tissue IHC), but verify antibody specificity because the catalog text describes GluR1 (datasheet: M01791).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
TFE3 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Mainly nuclear staining in tissue (HPA tissue IHC) | |
| Staining pattern | Glomerular and Leydig cells stain strongly; mainly nuclear (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep formalin fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Catalog specificity text describes GluR1; verify TFE3 staining (datasheet: M01791) | |
| Regulation | mTOR promotes TFE3 degradation (UniProt) | |
| Isoform / epitope | 2 isoforms; no transmembrane segment; epitope coverage unknown (UniProt; datasheet: M01791) |
Section 1
Recommended TFE3 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by 2 published TFE3 protocols with usable preparation or staining details (PMC12497915; PMC4884933).
| Sample | Paraffin-embedded human bladder tissue; fixative not specified (datasheet M01791) |
| Fixation | Image fixative and duration unreported (datasheet M01791); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit monoclonal (clone AFHC-20) anti-TFE3, 1:50-1:200 (datasheet M01791) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | TFE3-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous mainly nuclear expression. No signal in the no-primary control. |
💡Decision noteStart with the page’s Tris-EDTA pH 9.0 retrieval at 95–98 °C for 20 min (page antigen-retrieval rule); neither included excerpt specifies retrieval.
Section 2
What Is the Expected TFE3 Staining Pattern?
TFE3 is seen mainly in nuclei across many tissues, although its distribution can shift between nucleus and cytosol with nutrient state (HPA: ubiquitous mainly nuclear IHC profile; UniProt P19532: mTOR-regulated localisation). Strong IHC staining is reported in adrenal glandular cells, kidney glomerular cells, placental trophoblasts and testicular Leydig cells (HPA: High). HPA rates its tissue IHC profile Approved while noting low consistency between antibody staining and RNA expression (HPA: reliability description).
| Distinct nuclear staining in the expected cells, with readable counterstain and limited background. | This fits the mainly nuclear tissue pattern (HPA: tissue IHC profile). Compare intensity within the same section; High is an HPA category, not a universal chromogen threshold (HPA: High). |
| Cytosolic staining accompanies nuclear staining, or nuclear staining varies between fields. | TFE3 can occupy the cytosol, and nutrient signalling regulates its nuclear entry (UniProt P19532: subcellular location). Record both compartments before interpreting weaker nuclear staining as loss. |
| A crisp cell-surface outline dominates while nuclei of expected positive cells are blank. | A surface-only pattern is suspicious: TFE3 has no transmembrane segment, although it can associate with lysosomal membranes (UniProt P19532: topology and subcellular location). Check specificity and controls. |
| Signal is strongest in unexpected cells while the expected positive population is unstained. | Treat this as possible cross-reactivity or endogenous detection activity, not proof of TFE3 distribution. Compare with HPA's cell-level examples and its low RNA–staining consistency caveat (HPA: tissue IHC). |
| Diffuse staining obscures nuclei, or no signal appears in an expected positive population. | Neither result can be scored confidently. Use the strong cell-level HPA examples as comparators, while recognising that HPA reports observed patterns rather than performance guarantees for this section (HPA: High; reliability description). |
💡Expected TFE3 appearanceCall a section positive when expected cells show discernible, predominantly nuclear chromogenic staining with limited background; adrenal glandular cells or kidney glomerular cells are reported High examples (HPA: tissue IHC), whereas isolated surface outlines or uniform haze are suspect in light of TFE3 localisation (UniProt P19532: subcellular location and topology).
| Nutrient and lysosomal state (UniProt P19532: subcellular location). | With nutrients present, Rag-associated TFE3 can be recruited to lysosomal membranes and phosphorylated by mTOR; starvation or lysosomal disruption promotes nuclear translocation (UniProt P19532). Interpret nuclear-to-cytosolic balance in context. |
| Tissue and cell population (HPA: tissue IHC profile). | HPA reports High staining in esophageal squamous epithelial cells and placental trophoblasts, but Low staining in bronchial respiratory epithelial and lung alveolar cells (HPA: tissue IHC). Compare like cell types. |
| Antibody evidence (HPA: HPA023881 IHC Approved; tissue reliability description). | Approved status supports use as an IHC comparator, but HPA also reports low consistency with RNA expression (HPA: reliability description). An unexpected result needs slide-level controls and cautious interpretation. |
| Target forms and epitope (UniProt P19532: isoforms and processing). | Two isoforms are listed, with a single annotated chain spanning residues 1–575 and no signal peptide or propeptide (UniProt P19532). The supplied evidence gives no antibody epitope, so isoform-specific staining cannot be predicted. |
| Section preparation and detection (general IHC practice). | Antigen retrieval, primary concentration and chromogen development affect readability in paraffin IHC generally. No target-specific fixation sensitivity or retrieval condition is supplied for TFE3; optimise against controls without claiming a TFE3-specific effect. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected positive cells show no nuclear signal (HPA: High cell-level examples). | Possible assay failure, low sensitivity, or biological variation; the HPA category does not guarantee every specimen will stain (HPA: tissue IHC profile). | Verify that positive-control tissue and detection controls worked; review the antibody's supplied IHC-P instructions before adjusting retrieval or primary concentration (general IHC practice). |
| Brown haze covers nuclei and extracellular areas (general chromogenic IHC observation). | Excess detection signal or inadequate blocking or washing can produce nonspecific background (general IHC practice). | Compare a no-primary control, strengthen appropriate blocking and washing, and reduce detection development or primary concentration as the controls indicate (general IHC practice). |
| Only cells outside the expected positive population stain (HPA: cell-level tissue profile). | Cross-reactivity or endogenous enzyme activity is possible; widespread expression alone does not validate an unexpected cell pattern (UniProt P19532: tissue specificity). | Identify stained cells using morphology and counterstain; check no-primary and enzyme-block controls, then compare with HPA's cell-level examples (general IHC practice; HPA: tissue IHC). |
| A cell-surface rim is the dominant pattern (UniProt P19532: topology). | Surface staining does not match the mainly nuclear HPA pattern; lysosomal membrane association should not be equated with plasma-membrane localisation (HPA: tissue IHC; UniProt P19532). | Inspect nuclear signal and the no-primary control, then reassess antibody specificity and detection background before scoring the rim as TFE3 (general IHC practice). |
| Nuclear staining is weaker than cytosolic staining in an otherwise interpretable section (UniProt P19532: subcellular location). | Nutrient-dependent cytosolic retention is plausible, but staining alone cannot establish mTOR activity or the specimen's nutrient state (UniProt P19532: localisation mechanism). | Record nuclear and cytosolic staining separately and compare matched conditions; avoid assigning a signalling cause from compartment staining alone (UniProt P19532: localisation mechanism). |
| IF/ICC Q: What should a fluorescent TFE3 result show? (HPA: subcellular ICC-IF). | HPA supports nucleoplasmic localisation and rates cytosolic localisation uncertain in ICC-IF; these ratings describe IF evidence, not an IHC-P protocol (HPA: subcellular ICC-IF). | A: Look for nucleoplasmic signal with an appropriate nuclear counterstain, and interpret cytosolic fluorescence cautiously; use the separate IF/ICC guide for its workflow (HPA: subcellular ICC-IF). |
Experiment evidence
IHC & IF images showing TFE3 staining
M01791 · IHCImmunohistochemical analysis of paraffin-embedded human bladder, using TFE3 Antibody.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000068323-TFE3/tissue/cerebral+cortex#imid_6233692
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000068323-TFE3/tissue/colon#imid_6233330
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000068323-TFE3/tissue/liver#imid_6233323
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000068323-TFE3/tissue/kidney#imid_6233324
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA023881; green = TFE3, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA023881; green = TFE3, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for TFE3 IHC & IF
🧪Run kidney first and assess staining in glomerular cells (HPA: High in kidney glomerular cells). HPA detects TFE3 in all 45 scored tissues, so no tissue is a validated negative; use no-primary and isotype controls, and treat unstained neighboring cells on the kidney slide only as a background reference (HPA: no negative tissue rows).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: None in HPA: TFE3 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show TFE3 in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (supported), Cytosol (uncertain) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a host- and clonality-matched isotype control, and TFE3-knockout material as a biological negative (standard IHC/IF practice). For kidney chromogenic IHC, quench endogenous peroxidase and block endogenous biotin if using avidin–biotin detection (standard IHC practice).
⚠️Feasibility: A TFE3-specific fixation window or fixation effect is unreported, and the selected M01791 paraffin-section caption does not state a fixative (selected IHC caption). Retrieval dependence is unreported; optimize heat-induced antigen retrieval for paraffin IHC and assess nuclear staining (standard IHC practice; UniProt P19532: nucleus). HPA has ICC-IF images but provides no basis to rank frozen sections or IF as easier; in kidney, endogenous biotin can complicate avidin–biotin detection (HPA: ICC-IF images; standard IHC practice).
HPA tissue IHC evidence for TFE3
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
| Esophagus | Squamous epithelial cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in glomeruli | High | Protein (IHC) | HPA → |
| Placenta | Trophoblastic cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: TFE3 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced TFE3 IHC Tips
Troubleshoot TFE3 staining by checking nuclear signal, cell identity, section quality, and controls before comparing specimens (UniProt P19532; HPA tissue IHC).
Which retrieval conditions should I use when nuclear TFE3 staining is weak?
Use Tris-EDTA pH 9.0 heat-induced epitope retrieval at 95–98 °C for 20 min (page retrieval specification). Process a known positive control section alongside the sample, then compare nuclear signal and tissue preservation under identical detection conditions (standard IHC practice). If staining remains weak, adjust retrieval duration in a controlled series while keeping antibody dilution and detection constant (standard IHC practice). Document heating and cooling conditions because uneven retrieval can create regional staining differences that resemble biological variation (standard IHC practice). Assess nuclei first: TFE3 is a transcription factor with nuclear and cytosolic localisation (UniProt P19532; HPA subcellular).
How should I assess fixation as a cause of weak or patchy TFE3 staining?
Target-specific fixation sensitivity is unknown from the supplied evidence; the selected antibody image identifies paraffin-embedded human bladder but does not report its fixative (caption M01791). Record the actual fixative and fixation interval for each specimen, and compare sections processed together before changing the staining protocol (standard IHC practice). Check whether weak signal follows tissue edges, thick areas, or poorly preserved regions, and review morphology on the counterstained section (standard IHC practice). Use a similarly processed positive control to separate specimen-processing variation from a staining-run problem (standard IHC practice). Do not infer a fixation effect from TFE3 phosphorylation, topology, or HPA staining patterns (UniProt P19532; HPA tissue IHC).
Should I count cytoplasmic TFE3 staining as a positive IHC result?
Score nuclear and cytoplasmic staining separately because TFE3 occurs in both compartments, while HPA describes tissue staining as mainly nuclear (UniProt P19532; HPA tissue IHC). Nutrient-associated MTOR phosphorylation favors cytoplasmic retention, whereas starvation or lysosomal disruption promotes nuclear translocation (UniProt P19532). Compare cells within well-preserved areas and record compartment, intensity, and the fraction of cells stained before interpreting a change (standard IHC practice). A cytoplasmic-only result therefore needs context from sample handling and appropriate controls; it should not automatically be called absent TFE3 (UniProt P19532; standard IHC practice). Exclude diffuse precipitate and staining that ignores cell boundaries during review (standard IHC practice).
Can isoform choice or epitope placement explain discordant TFE3 staining?
TFE3 has 2 listed isoforms and a bHLH domain at residues 346–399, but the supplied antibody caption does not identify its epitope (UniProt P19532; caption M01791). Confirm the catalog antibody's immunogen and isoform coverage before attributing staining differences to a specific isoform (standard IHC practice). The record lists phosphorylation at residues including 47 and 321; epitope interference by these modifications remains unestablished for this antibody (UniProt P19532; caption M01791). If discordance persists, compare a second antibody with a documented, distinct epitope on serial sections and require matching cell-level patterns (standard IHC practice). Interpret differences only after retrieval and detection controls pass (standard IHC practice).
How can IF help resolve ambiguous TFE3 localisation seen by chromogenic IHC?
Use IF as a separate localisation check, pairing TFE3 with a validated marker for the expected cell population; HPA reports high staining in kidney glomerular cells (HPA tissue IHC; standard IF practice). Select spectrally separated fluorophores and place the weaker signal in a channel with low tissue autofluorescence, verified using an unstained section (standard IF practice). Include a nuclear counterstain and assess whether TFE3 overlaps nuclei or occupies cytosol; both compartments are reported (UniProt P19532; HPA subcellular). Because TFE3 has no transmembrane segment and can be nuclear, optimise permeabilisation for access across cellular and nuclear membranes (UniProt P19532; standard IF practice). Validate IF staining independently of the paraffin IHC caption (caption M01791).
What controls help distinguish TFE3 signal from chromogenic background?
Run a no-primary control and inspect it for secondary-reagent staining, endogenous peroxidase activity, and pigment before judging weak TFE3 signal (standard IHC practice). Apply a peroxidase block and optimise blocking, antibody dilution, washes, and DAB development using the same processing across controls and specimens (standard chromogenic IHC practice). Review whether colour is confined to cell structures rather than section folds, cut edges, necrotic areas, or pooled reagent (standard IHC practice). TFE3 may be cytosolic as well as nuclear, so cytoplasmic colour alone is insufficient evidence of background (UniProt P19532). Compare with a positive control and the no-primary section before adjusting thresholds (standard IHC practice).
How should I quantify TFE3 IHC when nuclear and cytoplasmic patterns differ? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, then report nuclear percent-positive cells and intensity or a nuclear H-score (standard IHC practice). Keep cytoplasmic staining as a separate measurement because TFE3 localisation changes with nutrient and MTOR signalling (UniProt P19532). If counting discrete positive cells, report density per mm² of viable tissue and state the area selection rule (standard IHC practice). Normalise positive counts to the number of evaluable cells in the same annotated population, and exclude necrosis, folds, and edge artefacts consistently (standard IHC practice). Apply one threshold and exposure or imaging setup across the comparison set (standard IHC practice).
When is strong TFE3 staining convincing rather than an artefact?
A convincing result follows identifiable cells, survives comparison with a no-primary control, and has a recorded nuclear or cytoplasmic pattern (standard IHC practice; UniProt P19532). Check cell identity against the specimen: HPA reports high staining in kidney glomerular cells and describes tissue expression as mainly nuclear (HPA tissue IHC). Treat colour concentrated at section edges, folds, necrotic regions, or sites of endogenous enzyme activity as suspect until controls resolve it (standard IHC practice). Nuclear enrichment can reflect TFE3 translocation during starvation or lysosomal disruption, but staining alone cannot establish the cause (UniProt P19532). HPA rates its tissue staining Approved while noting low consistency with RNA data, so corroborate consequential calls independently (HPA tissue IHC).
Boster reagents
Best TFE3 / Transcription factor E3 IHC Antibodies
M01791 is a human-reactive anti-TFE3 antibody with an IHC image of paraffin-embedded human bladder (catalog: reactivity, IHC image caption); IF/ICC is listed without an IF image (catalog: applications, IF image alts).
Real IHC data
Anti-TFE3 Monoclonal Antibody
Cat # M01791
M01791 will render with its own IHC image of paraffin-embedded human bladder (catalog: M01791 IHC image caption). It lists IHC and IF/ICC applications and human reactivity; no IF image is supplied (catalog: M01791 applications, reactivity, IF image alts).
Which to pick: Choose M01791 for human paraffin-section IHC because its own image caption documents that preparation in bladder tissue; the fixative is unreported (catalog: M01791 IHC image caption). For human IF/ICC, M01791 is the listed rabbit monoclonal option, with an IF dilution of 1:50–1:100 and no supplied IF image (catalog: M01791 host, clone, applications, reactivity, IF dilution, IF image alts). No cross-species choice is supported because M01791 lists human reactivity only (catalog: M01791 reactivity).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P19532 (TFE3_HUMAN, Transcription factor E3).
- Human Protein Atlas. TFE3 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. TFE3 subcellular location (ICC-IF): Localized to the nucleoplasm and cytosol..
- Human Protein Atlas. TFE3 antibody validation summary (1 antibodies).
- TFE3 immunohistochemistry in renal cell carcinomas: Does the clone really matter?. Northern clinics of Istanbul 2025 — PMC12497915.
- Epithelioid hemangioendotheliomas with TFE3 gene translocations are compossible with CAMTA1 gene rearrangements. Oncotarget 2016 — PMC4884933.
- The classification of pediatric and young adult renal cell carcinomas registered on the children's oncology group (COG) protocol AREN03B2 after focused genetic testing. Cancer 2018 — PMC6108909.
- TFE3 gene rearrangement and protein expression contribute to a poor prognosis of renal cell carcinoma. Heliyon 2023 — PMC10196445.
- PubMed PMID:9393982 — UniProt-cited evidence.
- PubMed PMID:17974005 — UniProt-cited evidence.
- PubMed PMID:15772651 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for TFE3 (Transcription factor E3). Expected localisation Mainly nuclear staining in tissue (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: M01791 at 1:50-1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative None in HPA (detected in all 45 tissues); use no-primary + isotype controls. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human bladder tissue; fixative not specified (datasheet M01791); 2. Fixation: Image fixative and duration unreported (datasheet M01791); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit monoclonal (clone AFHC-20) anti-TFE3, 1:50-1:200 (datasheet M01791); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep formalin fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Catalog specificity text describes GluR1; verify TFE3 staining (datasheet: M01791); Isoform / epitope: 2 isoforms; no transmembrane segment; epitope coverage unknown (UniProt; datasheet: M01791); Regulation: mTOR promotes TFE3 degradation (UniProt). Evidence: UniProt P19532, HPA tissue IHC · Approved, HPA ICC-IF · nucleoplasm and cytosol., Datasheet M01791, PMC12497915, PMC4884933. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/TFE3/immunohistochemistry-ihc-guide.