FTO / Alpha-ketoglutarate-dependent dioxygenase FTO · IHC design guide

Design Immunohistochemistry for FTO

Plan chromogenic FTO IHC on paraffin sections using nuclear staining as the tissue reference (HPA tissue IHC). Start with the IHC-validated antibody at 2–5 μg/mL (datasheet A00219-3), and compare high staining in adrenal glandular cells with low staining in hepatocytes (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for FTO (IHC for FTO): expected localisation Predominantly nuclear in tissue sections (HPA tissue IHC), antibody A00219-3, validated IHC image, and IHC protocol steps
Printable FTO IHC protocol sheet — expected localisation Predominantly nuclear in tissue sections (HPA tissue IHC), antibody A00219-3, controls and protocol steps. Open the full FTO IHC guide →

FTO 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 Predominantly nuclear in tissue sections (HPA tissue IHC)
Staining pattern General nuclear staining (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet A00219-3)
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 fixation conditions consistent across sections. (standard IHC practice; not target-specific)
Caveat Staining and RNA show medium consistency (HPA tissue IHC)
Regulation Elevated in select AML genotypes (UniProt)
Isoform / epitope 4 isoforms; verify epitope coverage (UniProt)
Section 1

Recommended FTO IHC & IF Protocols

The catalog antibody’s IHC-P protocol is accompanied by FTO IHC methods from three published articles (PMC9107638; PMC9792536; PMC12078176).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human colon cancer tissue; fixative not specified (datasheet A00219-3)
FixationImage fixative and duration unreported (datasheet A00219-3); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet A00219-3); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A00219-3)
Primary antibodyRabbit anti-FTO, 2-5μg/ml (datasheet A00219-3)
Primary incubationOvernight at 4 °C (datasheet A00219-3)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet A00219-3)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultFTO-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: General nuclear expression. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A00219-3); Tris-EDTA pH 9.0 is a published FTO alternative (PMC9792536).
Section 2

What Is the Expected FTO Staining Pattern?

FTO shows general nuclear staining in tissue IHC, with high staining in adrenal glandular cells, cerebellar granular-layer cells, and duodenal Paneth cells (HPA: tissue IHC). UniProt places FTO mainly in the nucleus, with additional cytoplasmic localization; it has no transmembrane segment (UniProt Q9C0B1: localization and topology). HPA rates the tissue IHC profile Enhanced, while reporting medium consistency between antibody staining and RNA expression (HPA: tissue IHC).

What am I looking at on my slide?
Nuclear staining in glandular cells of adrenal gland or Paneth cells of duodenum (HPA: High in both).This fits the reported tissue IHC pattern and UniProt's mainly nuclear localization (HPA: general nuclear expression; UniProt Q9C0B1). Compare staining across cells within the section; a positive control supports interpretation of the run (standard IHC practice).
Predominantly membrane-associated staining, with little nuclear signal.FTO has no transmembrane segment and is mainly nuclear by UniProt; HPA tissue IHC also reports general nuclear expression (UniProt Q9C0B1: topology and localization; HPA: tissue IHC). Review this pattern for nonspecific staining or a detection artefact (standard IHC practice).
Strong staining appears only in an unexpected cell population.Assess the cell identity and controls before calling it FTO: HPA reports low tissue specificity and staining in multiple cell types (HPA: tissue IHC). Cross-reactivity or endogenous detection activity is possible, especially if the expected nuclear pattern is absent (standard IHC practice).
Diffuse color covers nuclei, cytoplasm, and tissue spaces without clear cell boundaries.That distribution cannot establish FTO localization (standard IHC practice). Background from the detection system or insufficient blocking or washing can obscure the nuclear pattern expected in tissue IHC (HPA: general nuclear expression; standard IHC practice).
No visible signal in an adrenal gland section's glandular cells.HPA reports high staining in these cells, so a blank result calls for a technical check (HPA: adrenal gland tissue IHC). Review the positive control, primary antibody, retrieval, and detection steps before interpreting the section as FTO-negative (standard IHC practice).
💡Expected FTO appearanceA convincing positive is cell-resolved, predominantly nuclear staining, potentially high in adrenal glandular cells or duodenal Paneth cells; diffuse color or membrane-only staining warrants investigation (HPA: tissue IHC; UniProt Q9C0B1: localization and topology; standard IHC practice).
How each factor affects the staining
Tissue and cell choice (HPA: tissue IHC)Adrenal glandular cells, cerebellar granular-layer cells, and duodenal Paneth cells have high reported staining (HPA: tissue IHC). Hepatocytes and adipocytes are reported low, which makes them weaker positive benchmarks, rather than established negatives (HPA: tissue IHC).
IHC versus ICC-IF localization (HPA: tissue IHC and subcellular ICC-IF)Q: What if IF appears cytosolic? A: HPA ICC-IF supports cytosol as the main location and also reports vesicles, whereas its tissue IHC profile is generally nuclear (HPA: subcellular ICC-IF; HPA: tissue IHC). Compare each result with its own application evidence; UniProt also lists cytoplasm (UniProt Q9C0B1: localization).
Antibody evidence (HPA: antibody validation)HPA041086 and HPA068695 each have Enhanced IHC validation (HPA: antibodies). That supports using their reported staining patterns as references, while HPA's tissue summary still notes medium consistency with RNA expression (HPA: tissue IHC). Match any catalog antibody to its own documented IHC-P validation (standard IHC practice).
Protein forms and epitope information (UniProt Q9C0B1)UniProt lists four isoforms and one annotated chain spanning residues 1–505, with no signal peptide or propeptide (UniProt Q9C0B1: isoforms and processing). The supplied evidence does not map a catalog antibody epitope; isoform coverage and epitope-specific staining therefore remain unresolved.
Endogenous chromogenic activity (standard IHC practice)Native tissue activity can produce chromogenic signal independently of primary antibody binding (standard IHC practice). A suitable no-primary control helps identify detection-derived staining; interpret residual color against the cell-resolved nuclear pattern reported for FTO tissue IHC (HPA: tissue IHC; standard IHC practice).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Expected positive cells remain blank (HPA: High in adrenal glandular cells).The staining run may have failed, or the selected conditions may not detect the antigen in that section (standard IHC practice).Confirm tissue and cell identity, check a known-positive control, then review primary antibody application, retrieval, and chromogenic detection records (HPA: tissue IHC; standard IHC practice). No FTO-specific retrieval condition is established here.
Signal is mostly membrane-associated, without the expected nuclear pattern (HPA: tissue IHC).This conflicts with general nuclear tissue staining and the lack of a transmembrane segment (HPA: tissue IHC; UniProt Q9C0B1: topology); nonspecific detection is possible (standard IHC practice).Compare with a no-primary control and an HPA-supported positive cell population; re-evaluate antibody specificity if the membrane pattern persists (HPA: tissue IHC; standard IHC practice).
Brown color is widespread, including tissue spaces (standard IHC practice).Detection background can conceal cell boundaries and subcellular localization (standard IHC practice).Inspect the no-primary control, blocking, wash steps, and development time; score FTO only where cell-associated staining can be distinguished (standard IHC practice).
Only unexpected cell types stain strongly.HPA reports low tissue specificity, so cell identity alone cannot establish an artefact; cross-reactivity or endogenous activity remains possible (HPA: tissue IHC; standard IHC practice).Check the nuclear pattern, tissue morphology, and no-primary control, then compare with HPA's reported cell-level staining before assigning FTO positivity (HPA: tissue IHC; standard IHC practice).
A low-staining tissue gives little or no usable signal (HPA: Low in hepatocytes and adipocytes).Those HPA observations provide a limited positive benchmark (HPA: tissue IHC).Assess the run in a reported high population, such as adrenal glandular cells, before drawing a conclusion from the low-staining tissue (HPA: tissue IHC; standard IHC practice).
Results differ between antibodies or between tissue IHC and ICC-IF.HPA reports medium tissue IHC–RNA consistency, while its ICC-IF localization is mainly cytosolic (HPA: tissue IHC; HPA: subcellular ICC-IF).Record the antibody and application, compare like with like, and use an independently validated IHC pattern when available (HPA: antibody validation; standard IHC practice). Treat unresolved compartment differences as an interpretation limit.

Sample controls for FTO IHC & IF

🧪Run adrenal gland first: its glandular cells should stain for FTO (HPA: High in adrenal gland glandular cells). HPA detects FTO in all 45 scored tissues, so there is no documented negative tissue; use no-primary and isotype controls, and treat acellular spaces on the positive slide as a background check rather than calling any cell population FTO-negative (HPA: no negative rows; standard IHC practice).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: None in HPA: FTO 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 FTO in A-431, U-251MG, U2OS, HeLa, Hep-G2, with annotated localisation: Cytosol (supported) (HPA subcellular).
Technical controls: Run a secondary-only section with the primary omitted and a section with concentration-matched rabbit control IgG in place of the rabbit primary; where available, use FTO knockout material as a biological negative (A00219-3 caption: rabbit primary; standard IHC practice). Quench endogenous peroxidase and check for endogenous biotin when using the caption’s biotin–SABC–DAB detection system (A00219-3 caption: biotinylated secondary, SABC and DAB; standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the fixative for the selected paraffin-section example is unreported (A00219-3 caption: fixative not stated). That example uses heat retrieval in EDTA at pH 8.0, but it does not establish that retrieval is required for every specimen (A00219-3 caption: EDTA retrieval). The supplied evidence does not establish whether frozen sections or IF are easier; in adrenal sections, inspect pigment and blood-associated color separately from DAB signal (supplied evidence: IHC caption only; standard IHC practice).

HPA tissue IHC evidence for FTO

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium 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

TissueCell typeLevelEvidenceSource
Adrenal gland Glandular cells High Protein (IHC) HPA →
Cerebellum Cells in granular layer High Protein (IHC) HPA →
Cervix Glandular cells High Protein (IHC) HPA →
Duodenum Paneth cells High Protein (IHC) HPA →
Epididymis Glandular cells High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
None in HPA: FTO is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced FTO IHC Tips

Troubleshoot FTO staining in paraffin sections by checking retrieval, compartment, controls, and scoring before interpreting changes in expression.

How should I retrieve FTO antigen when nuclear staining is weak?
Start with heat-mediated retrieval in EDTA at pH 8.0 (datasheet A00219-3). The selected paraffin-section image used this retrieval before incubation with 2 μg/ml antibody overnight at 4°C (caption A00219-3). Keep section thickness, heating, cooling, and detection conditions consistent while adjusting retrieval time in small steps (standard IHC practice). Compare the trial sections with a concurrently processed positive control, since absent nuclear signal could also reflect antibody incubation or detection failure (standard IHC practice; UniProt Q9C0B1 localisation). Record both nuclear and cytoplasmic staining, as FTO has reported localisation in each compartment (UniProt Q9C0B1 localisation).
Could fixation explain weak or uneven FTO staining?
Target-specific sensitivity of FTO to fixation is unknown from the supplied evidence; the selected paraffin-section caption does not state a fixative (caption A00219-3). For new specimens, document fixative, fixation duration, and tissue thickness, then process comparison sections together (standard IHC practice). Excessive or uneven fixation can alter antigen accessibility in IHC generally, so compare matched sections before changing the antibody concentration (standard IHC practice). Use the documented EDTA pH 8.0 retrieval and 2 μg/ml primary incubation as reference conditions (caption A00219-3). Do not assign a fixation effect to FTO from its nuclear localisation or modified residues alone (UniProt Q9C0B1 localisation and modified residues).
Should FTO staining be nuclear or cytoplasmic in paraffin sections?
Assess nuclei first: tissue IHC reports general nuclear expression, and UniProt describes FTO as mainly nuclear, including nuclear speckles (HPA tissue IHC; UniProt Q9C0B1 localisation). Also record cytoplasmic staining because UniProt reports cytoplasmic FTO, while HPA cell-image data support a mainly cytosolic location with additional vesicular signal (UniProt Q9C0B1 localisation; HPA subcellular). These sources describe different observations, so apply the same compartment definitions and counterstain across every section in the comparison (standard IHC practice). Review high-magnification fields for genuine intracellular signal before assigning a compartment, particularly where adjacent cells overlap (standard IHC practice). Report nuclear and cytoplasmic scores separately rather than collapsing them into one positive-cell count (standard IHC practice).
Could FTO isoforms or epitope accessibility change the staining pattern?
FTO has 4 annotated isoforms, but the supplied antibody caption does not map its epitope or establish which isoforms it detects (UniProt Q9C0B1 isoforms; caption A00219-3). Therefore, a change in staining cannot be assigned to a particular isoform from this IHC assay alone (UniProt Q9C0B1 isoforms; standard IHC interpretation). The canonical protein has no annotated transmembrane segment or signal peptide, and its listed modifications include phosphothreonine at position 4 and acetyllysine at position 216 (UniProt Q9C0B1 topology, processing, and modified residues). Those annotations do not show whether the antibody recognises either modified site (caption A00219-3; UniProt Q9C0B1 modified residues). Obtain epitope mapping or orthogonal validation before making isoform-specific claims (standard IHC practice).
How can IF help resolve ambiguous FTO staining?
For a separate IF experiment, multiplex FTO with a marker identifying the expected cell population, such as adrenal glandular cells, and compare the channels within individual cells (HPA tissue IHC; standard IF practice). Choose spectrally separated fluorophores and place the weaker signal in a red or far-red channel after checking tissue autofluorescence (standard IF practice). FTO lacks a transmembrane segment; permeabilise cellular membranes for cytosolic access and ensure nuclear access when assessing the nuclear pool, while recognising that the antibody's epitope is unmapped here (UniProt Q9C0B1 topology and localisation; caption A00219-3; standard IF practice). Include single-colour and secondary-only controls to identify channel bleed-through and nonspecific signal (standard IF practice). Do not treat the paraffin-section caption as IF validation (caption A00219-3).
What should I check when FTO DAB staining looks diffuse?
First compare the stain with a no-primary control and inspect the nuclear counterstain to distinguish cellular signal from diffuse chromogen (standard IHC practice). The selected image used 10% goat-serum blocking, biotinylated goat anti-rabbit secondary antibody, a streptavidin-biotin complex, and DAB (caption A00219-3). In that detection scheme, check endogenous peroxidase and tissue biotin with appropriate controls; peroxidase blocking is a general DAB workflow step (standard IHC practice). Reduce excessive background by optimising blocking, washes, primary incubation, and chromogen development one variable at a time (standard IHC practice). Preserve a concurrently processed positive control so loss of background is not mistaken for improved FTO detection (standard IHC practice).
How should I score FTO across heterogeneous tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, then report nuclear and cytoplasmic results separately (standard IHC practice; UniProt Q9C0B1 localisation). A nuclear H-score combines the percentage of cells at intensity 0–3, yielding a possible range of 0–300; also report the percentage positive if that better fits the question (standard IHC practice). Normalise each result to the number of eligible, intact cells assessed, or use positive-cell density per mm² of viable tissue when cell counts are impractical (standard IHC practice). Apply one positivity threshold, imaging setup, and sampling rule across sections, and document excluded necrotic or damaged areas (standard IHC practice). Keep cell populations separate because reported FTO staining varies among tissue cell types (HPA tissue IHC).
How do I distinguish true FTO staining from artefact?
Treat staining as more credible when it is intracellular, reproducible across intact cells, and consistent with nuclear FTO reported by tissue IHC and UniProt (HPA tissue IHC; UniProt Q9C0B1 localisation; standard IHC practice). Cytoplasmic signal can also be plausible, but should be scored separately because HPA cell-image data support cytosolic localisation (UniProt Q9C0B1 localisation; HPA subcellular). Check whether the stained cells match the intended population; HPA reports high staining in adrenal glandular cells but low staining in liver hepatocytes, for example (HPA tissue IHC). Discount staining confined to tissue edges or necrotic areas, and investigate signal in no-primary controls for endogenous enzyme or detection background (standard IHC practice). A single unexpected compartment or cell pattern warrants independent validation before a biological conclusion (standard IHC practice).
Boster reagents

Best FTO / Alpha-ketoglutarate-dependent dioxygenase FTO IHC Antibodies

Anti-FTO antibodies cover human, mouse, and rat reactivity (catalog reactivity), with IHC images from human and mouse tissues and IF images from cells or an unspecified sample (catalog image captions).

Real IHC data IHC analysis of FTO using anti-FTO antibody (A00219-3). FTO was detected in a paraffin-embedded section of human colon cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-FTO Antibody (A00219-3) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1022) with DAB as the chromogen.
Anti-FTO Antibody ®
Cat # A00219-3
Real IHC data Immunohistochemistry of FTO in mouse brain tissue with FTO antibody at 2.5 μg/mL.
Anti-FTO Antibody
Cat # A00219
Real IHC data Human kidney was stained with anti-FTO rabbit antibody
Anti-FTO Rabbit Monoclonal Antibody
Cat # M00219-2
Real IF data Immunofluorescent analysis using the Antibody at 1:50 dilution.
Anti-FTO Monoclonal Antibody
Cat # M00219

A00219-3 shows paraffin-section IHC in human colon cancer at 2 μg/mL (catalog IHC caption); A00219 shows mouse brain IHC at 2.5 μg/mL, although its reactivity listing names only Human (catalog IHC caption; catalog reactivity). M00219-2 shows human kidney IHC (catalog IHC caption); M00219 has an IF image at 1:50 with no sample identified (catalog IF caption).

Which to pick: For tissue IHC, A00219-3 has a documented paraffin-section example with EDTA retrieval at pH 8.0; the fixative is unreported (catalog IHC caption). For IF/ICC, A00219-3 has a U2OS cell image at 5 μg/mL, while M00219 lists both applications but does not identify the sample in its IF caption (catalog applications; catalog IF captions). For cross-species IHC, A00219-3 has Human, Mouse, and Rat reactivity plus mouse and rat brain IHC captions; M00219-2 lists the same species but its IHC caption identifies only human kidney (catalog reactivity; catalog IHC captions).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q9C0B1 (FTO_HUMAN, Alpha-ketoglutarate-dependent dioxygenase FTO).
  2. Human Protein Atlas. FTO tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. FTO subcellular location (ICC-IF): Mainly localized to the cytosol. In addition localized to vesicles..
  4. Human Protein Atlas. FTO antibody validation summary (3 antibodies).
  5. m6A demethylase FTO promotes tumor progression via regulation of lipid metabolism in esophageal cancer. Cell & bioscience 2022 — PMC9107638.
  6. A study of RNA m6A demethylases in oral epithelial dysplasia and oral squamous cell carcinoma. Journal of oral biology and craniofacial research 2023 — PMC9792536.
  7. FTO-CHRM3 axis regulates multiple myeloma progression: a machine learning-based identification. Annals of hematology 2026 — PMC13009012.
  8. FTO Promotes Hepatocellular Carcinoma Progression by Mediating m6A Modification of BUB1 and Targeting TGF-βR1 to Activate the TGF-β Signaling Pathway. Journal of clinical and translational hepatology 2025 — PMC12078176.
  9. PubMed PMID:11214970 — UniProt-cited evidence.
  10. PubMed PMID:15616553 — UniProt-cited evidence.
  11. PubMed PMID:15489334 — UniProt-cited evidence.