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APIP / Methylthioribulose-1-phosphate dehydratase · IHC design guide
Design Immunohistochemistry for APIP
Plan APIP staining in paraffin sections using the reported nuclear and cytoplasmic tissue pattern (HPA tissue IHC). Use high-staining glandular cells as positive controls and score each cell type separately (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
APIP 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 | Nuclear and cytoplasmic tissue staining (HPA tissue IHC) | |
| Staining pattern | Variable nuclear and cytoplasmic staining across tissues (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Cerebellum+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Staining varies by tissue and cell type (HPA tissue IHC) | |
| Regulation | Isoform 2 is expressed at lower levels (UniProt) | |
| Isoform / epitope | Two isoforms; their epitope coverage is unknown (UniProt) |
Section 1
Recommended APIP IHC & IF Protocols
The catalog antibody’s IHC-P protocol appears alongside a published APIP protocol for HCC paraffin sections (PMC12541992).
| Sample | Paraffin-embedded human colon tissue; fixative not specified (datasheet A09029) |
| Fixation | Image fixative and duration unreported (datasheet A09029); 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 citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane 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 anti-APIP, 1:50-1:200 (datasheet A09029) |
| 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 | APIP-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Nuclear and cytoplasmic expression at variable levels in several different tissue types. No signal in the no-primary control. |
💡Decision noteTry citrate pH 6.0 HIER at 95–98 °C for 20 min first (page retrieval rule; UniProt Q96GX9: cytoplasm). The paper used high-pressure citrate retrieval (PMC12541992).
Section 2
What Is the Expected APIP Staining Pattern?
APIP should stain glandular cells in several tissues, with high IHC staining reported in colon, pancreas, stomach and other listed glands (HPA: tissue IHC). Nuclear and cytoplasmic staining is reported across tissues (HPA: Approved; medium consistency with RNA). Cytoplasmic localization is annotated by UniProt; APIP has no transmembrane segment or signal peptide (UniProt Q96GX9).
| Glandular cells show distinct nuclear and cytoplasmic chromogen in a positive tissue. | This fits the variable nuclear and cytoplasmic IHC profile (HPA: tissue IHC). Compare cells within the section: HPA reports High staining in colon glandular cells and pancreatic exocrine glandular cells (HPA: tissue IHC). |
| Staining is confined to cell borders or extracellular material, with no convincing intracellular signal. | Recheck specificity and section quality. The reported IHC pattern is nuclear and cytoplasmic (HPA: tissue IHC); UniProt lists cytoplasm and no transmembrane segment or signal peptide (UniProt Q96GX9). A border-only pattern is therefore unsupported. |
| Strong staining appears chiefly in cells outside the expected positive population. | Treat it as a possible specificity or detection problem, then compare morphology and a no-primary control. For example, HPA reports high staining in colon glandular cells but no detection in cerebellar granular-layer cells (HPA: tissue IHC). These observations are cell-specific. |
| Chromogen spreads uniformly across tissue, including spaces between cells. | Diffuse staining obscures the reported intracellular pattern (HPA: tissue IHC). Review background and detection controls before scoring APIP; broad color alone cannot establish expression in a particular cell type (general IHC interpretation). |
| No signal is seen in the expected positive glandular cells. | First verify the tissue and cell population: colon glandular cells and pancreatic exocrine glandular cells are reported High (HPA: tissue IHC). An absent result calls for checking antibody, detection and run controls; it does not alone establish absent APIP. |
💡Expected APIP appearanceCall a positive result when glandular cells show clear intracellular nuclear and cytoplasmic staining, potentially High in colon or pancreatic exocrine cells (HPA: tissue IHC); isolated cell-border or extracellular color is an unsupported pattern (HPA: tissue IHC; UniProt Q96GX9 topology).
| Tissue and cell selection | HPA reports High staining in glandular cells of adrenal gland, colon, gallbladder, prostate, salivary gland, small intestine and stomach, plus pancreatic exocrine cells (HPA: tissue IHC). Select and score the specified cells, rather than treating an entire organ as uniformly positive. |
| Interpretation of low or undetected cells | HPA lists low staining in thyroid glandular cells and no detection in cervix glandular cells (HPA: tissue IHC). These are observed cell-level results, not proof that every cell or section from those organs must be negative. |
| Compartment and topology | Tissue IHC describes variable nuclear and cytoplasmic expression (HPA: tissue IHC), while UniProt annotates cytoplasm and no transmembrane segment or signal peptide (UniProt Q96GX9). Use the tissue IHC observation for slide scoring; investigate a solely membranous pattern. |
| Isoforms and protein processing | Isoform 1 is ubiquitous; isoform 2 is lower and detected in selected tissues (UniProt Q96GX9). UniProt annotates a single 1–242 chain and no signal peptide or propeptide (UniProt Q96GX9). Antibody recognition of each isoform is unspecified here. |
| Validation and IF/ICC applicability | Q: Should IF/ICC match the tissue IHC result? A: HPA reports mainly nucleoplasm plus cytosol in ICC-IF (HPA: subcellular). Its tissue IHC rating is Approved with medium RNA consistency (HPA: tissue IHC); HPA021188 has Uncertain ICC validation (HPA: antibodies). |
| Situation | Likely cause | Next action |
|---|---|---|
| Positive-control glandular cells have no chromogen. | The expected cell population may be missing, or an IHC reagent or detection step may have failed; absent color alone cannot identify which (general IHC practice). | Confirm the cells on the section, then review the antibody and detection run controls. Use a reported high-staining population such as colon glandular cells (HPA: tissue IHC). |
| All cells stain similarly, including a population expected to be undetected. | Nonspecific binding or detection background may mask cell-specific staining (general IHC practice). HPA reports no detection in cerebellar granular-layer cells (HPA: tissue IHC). | Compare a no-primary control and assess background before interpreting the section. Keep the HPA comparison tied to the named cell population, not the whole cerebellum (HPA: tissue IHC). |
| The signal appears only at plasma membranes. | A compartment mismatch raises concern for nonspecific staining or misidentified morphology (general IHC interpretation); APIP has no annotated transmembrane segment (UniProt Q96GX9). | Re-examine the counterstained cell boundaries and compare the positive control. Score nuclear and cytoplasmic intracellular signal against the reported IHC profile (HPA: tissue IHC). |
| A negative-looking area is interpreted as a failed APIP stain. | The sampled cells may normally have low or undetected IHC staining: HPA reports low signal in cerebral-cortex glia and no detection in ovarian stroma cells (HPA: tissue IHC). | Identify the exact cell type, then check a reported high-staining glandular population in the same run (HPA: tissue IHC). Do not infer assay failure from one low-staining population. |
| Nuclear staining is rejected because the UniProt location says cytoplasm. | The records describe different evidence: UniProt annotates cytoplasm (UniProt Q96GX9), and HPA observes variable nuclear and cytoplasmic staining in tissue IHC (HPA: tissue IHC). | Record nuclear and cytoplasmic compartments separately, and judge the pattern with tissue morphology and controls. Do not discard nuclear staining solely from the UniProt annotation. |
| An IF/ICC image is used to validate an IHC section directly. | ICC-IF localization and antibody validation do not automatically transfer to tissue IHC; HPA021188 is IHC Approved but ICC Uncertain (HPA: antibodies). | Interpret the paraffin-section result against HPA tissue IHC and its cell-level controls (HPA: tissue IHC). Use the ICC-IF nucleoplasm and cytosol result only as context (HPA: subcellular). |
Experiment evidence
IHC & IF images showing APIP staining
A09029 · IHCImmunohistochemistry of paraffin-embedded human colon using APIP Rabbit pAb at dilution of 1:100 .Perform microwave antigen retrieval with 1
A09029 · IHCImmunohistochemistry of paraffin-embedded mouse liver using APIP Rabbit pAb at dilution of 1:100 .Perform microwave antigen retrieval with 1
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000149089-APIP/tissue/cerebral+cortex#imid_7919832
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000149089-APIP/tissue/colon#imid_7917246
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000149089-APIP/tissue/liver#imid_7917247
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000149089-APIP/tissue/kidney#imid_7917256
HPA · ICC-IF PC-3Human Protein Atlas immunofluorescence, PC-3, antibody HPA021188; green = APIP, blue = nucleus, red = microtubules.
HPA · ICC-IF PC-3Human Protein Atlas immunofluorescence, PC-3, antibody HPA021188; green = APIP, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for APIP IHC & IF
🧪Run colon first: its glandular cells should stain (HPA: High in colon glandular cells). Run cervix glandular cells as the tissue negative (HPA: Not detected); on the colon slide, internal negative cells should show counterstain without specific chromogen, although the supplied HPA row does not identify a verified negative colon cell type.
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: Cerebellum (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show APIP in PC-3, Rh30, U2OS, with annotated localisation: Nucleoplasm (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a matched rabbit IgG isotype control for the catalog rabbit polyclonal antibody, and APIP-knockout material if available as a biological negative (caption: rabbit pAb; standard IHC practice). Quench endogenous peroxidase in colon sections and block endogenous biotin if using avidin-biotin detection (standard chromogenic IHC practice).
⚠️Feasibility: The selected A09029 paraffin-section colon caption uses microwave retrieval in 10 mM PBS at pH 7.2 with antibody at 1:100; it does not establish that retrieval is essential (selected-SKU tissue-IHC caption). A target-specific fixation window or fixation effect is unreported, and the caption does not report a fixative (selected-SKU tissue-IHC caption). The supplied evidence does not establish whether frozen sections or IF would be easier; in colon, check apparent luminal or mucus-associated signal against morphology and negative controls (standard IHC practice).
HPA tissue IHC evidence for APIP
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — 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
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Gallbladder | Glandular cells | High | Protein (IHC) | HPA → |
| Pancreas | Exocrine glandular cells | High | Protein (IHC) | HPA → |
| Prostate | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
| Cervix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Hippocampus | Glial cells | Not detected | Protein (IHC) | HPA → |
| Ovary | Ovarian stroma cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced APIP IHC Tips
Troubleshoot APIP staining by checking retrieval, compartment, cell type and controls before comparing signal across sections.
How should I adjust retrieval when APIP staining is weak in paraffin sections?
Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 minutes (page retrieval setting). If staining remains weak, compare a serial section using microwave retrieval in 10 mM PBS, pH 7.2, the condition reported for the A09029 paraffin colon image (A09029 image caption). Keep antibody concentration, detection and development time identical across sections so the retrieval comparison is interpretable (standard IHC practice). Check tissue morphology and staining in both a positive control and a no-primary control before increasing retrieval intensity, which can damage sections or raise background (standard IHC practice).
Could fixation explain weak or uneven APIP staining?
APIP-specific sensitivity to fixation is unknown because the supplied A09029 paraffin-section caption does not state a fixative (A09029 image caption). Record the fixative, fixation duration and processing history for each specimen, then compare sections processed alike before attributing a difference to APIP expression (standard IHC practice). Where tissue history varies, run a matched positive control alongside each batch and assess morphology as well as staining (standard IHC practice). Avoid treating retrieval as a complete correction for unknown fixation differences; evaluate a small retrieval series while holding the 1:100 antibody dilution reported for A09029 constant (A09029 image caption; standard IHC practice).
Should nuclear staining be accepted when APIP is described as cytoplasmic?
Score nuclear and cytoplasmic staining separately: UniProt lists APIP in the cytoplasm, while HPA reports nuclear and cytoplasmic tissue staining and approved nucleoplasmic plus cytosolic subcellular localisation (UniProt Q96GX9; HPA tissue IHC; HPA subcellular). Assess each compartment against matched no-primary controls and the surrounding cell morphology before calling it positive (standard IHC practice). Compare glandular cells in colon, which HPA scores High, with cells in the cerebellar granular layer, which HPA scores Not detected (HPA tissue IHC). Do not force both compartments into one score when their staining differs; document the compartment and cell population used for each comparison (standard IHC practice).
Can this antibody distinguish APIP isoforms in tissue sections?
The supplied evidence identifies 2 APIP isoforms but gives no epitope map or isoform-specific validation for the catalog antibody (UniProt Q96GX9; supplied antibody evidence). Treat IHC staining as APIP-associated signal without assigning it to isoform 1 or 2 on staining pattern alone (standard IHC interpretation). UniProt describes isoform 1 as ubiquitous and isoform 2 as lower-level in specified tissues, including pancreas and liver (UniProt Q96GX9). If isoform identity matters, obtain an epitope sequence and validate recognition with an independent isoform-resolving method before interpreting differences between sections (standard antibody-validation practice).
How can IF help resolve an ambiguous APIP IHC pattern?
Use IF on a matched specimen as a localisation check, and multiplex APIP with a validated glandular-cell marker where assessing the High glandular-cell staining reported in colon (HPA tissue IHC; standard IF practice). Choose fluorophores after inspecting tissue autofluorescence, favouring a well-separated, longer-wavelength detection channel for a dim APIP signal (standard IF practice). Because APIP has no annotated transmembrane segment and has cytosolic and nucleoplasmic localisation evidence, permeabilise cells sufficiently to access intracellular epitopes while preserving morphology (UniProt Q96GX9; HPA subcellular; standard IF practice). Include single-colour and no-primary controls to assess bleed-through and background; interpret the IF pattern alongside chromogenic IHC rather than transferring its signal threshold directly (standard IF practice).
What should I change if APIP staining appears diffuse across the section?
First inspect the no-primary control for diffuse chromogen, then check peroxidase blocking and wash steps before changing the APIP antibody concentration (standard chromogenic IHC practice). Compare serial sections developed for the same time, since unequal development can make background resemble weak cytoplasmic staining (standard IHC practice). Reassess the reported 1:100 dilution for A09029 in a small dilution series while keeping retrieval fixed, and record whether specific cellular contrast improves (A09029 image caption; standard IHC practice). Judge any apparent improvement in a cell population with expected signal, such as colon glandular cells, alongside a no-primary section (HPA tissue IHC; standard IHC practice).
How should APIP staining be scored across samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the tissue compartment and cell population before scoring, because HPA reports variable nuclear and cytoplasmic expression across tissues (HPA tissue IHC). For glandular cells, record the percentage positive and an intensity-based H-score for nucleus and cytoplasm separately, using the same scoring thresholds across slides (standard IHC quantification practice). If counting positive cells, report density per mm² of viable, evaluable tissue and normalise percentages to the relevant cell population rather than the whole section (standard IHC quantification practice). Keep retrieval, imaging and chromogen development consistent, and exclude folds, edges and necrotic areas using prespecified criteria (standard IHC quantification practice).
How can I distinguish genuine APIP staining from artefact?
Look for reproducible staining within intact cells and compare its nuclear or cytoplasmic distribution with the reported APIP patterns (HPA tissue IHC; HPA subcellular; standard IHC practice). Colon glandular cells provide a High-staining reference, whereas cells in the cerebellar granular layer were Not detected in HPA tissue IHC; differences between sources still require matched assay controls (HPA tissue IHC; standard IHC practice). Discount signal confined to section edges, folds or necrotic regions, and inspect the no-primary control for endogenous enzyme activity or detection background (standard chromogenic IHC practice). When an unexpected cell type or compartment stains strongly, confirm it on a serial section and with an independent antibody or method before making a biological claim (standard antibody-validation practice).
Boster reagents
Best APIP / Methylthioribulose-1-phosphate dehydratase IHC Antibodies
A09029 has IHC images from paraffin sections of human colon and mouse liver; no IF image is supplied (A09029 IHC image captions; catalog IF images).
Real IHC data
Anti-APIP Antibody
Cat # A09029
A09029 is listed for IHC and has staining images from paraffin sections of human colon and mouse liver (A09029 catalog applications; IHC image captions). Its listed reactivity is Human, Mouse and Rat, while the supplied IHC images show human and mouse specimens (A09029 catalog reactivity; IHC image captions).
Which to pick: For tissue IHC, choose A09029, a rabbit polyclonal antibody whose captions show paraffin-section staining at 1:100 after microwave retrieval in 10 mM PBS at pH 7.2; the fixative is unreported (A09029 catalog host; IHC image captions). For IF/ICC, A09029 has no listed IF application or IF image (A09029 catalog applications; IF images). For cross-species work, A09029 lists Human, Mouse and Rat reactivity, with IHC images supplied for human and mouse specimens (A09029 catalog reactivity; IHC image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q96GX9 (MTNB_HUMAN, Methylthioribulose-1-phosphate dehydratase).
- Human Protein Atlas. APIP tissue IHC expression (reliability: Approved).
- Human Protein Atlas. APIP subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the cytosol..
- Human Protein Atlas. APIP antibody validation summary (2 antibodies).
- Clinical pathological significance and biological functions of APIP in hepatocellular carcinoma. Cancer cell international 2025 — PMC12541992.
- PubMed PMID:10810093 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:16554811 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for APIP (Methylthioribulose-1-phosphate dehydratase). Expected localisation Nuclear and cytoplasmic tissue staining (HPA tissue IHC). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: A09029 at 1:50-1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative Cerebellum. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human colon tissue; fixative not specified (datasheet A09029); 2. Fixation: Image fixative and duration unreported (datasheet A09029); 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 citrate buffer, pH 6.0 , 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 anti-APIP, 1:50-1:200 (datasheet A09029); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Staining varies by tissue and cell type (HPA tissue IHC); Isoform / epitope: Two isoforms; their epitope coverage is unknown (UniProt); Regulation: Isoform 2 is expressed at lower levels (UniProt). Evidence: UniProt Q96GX9, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet A09029, PMC12541992. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/APIP/immunohistochemistry-ihc-guide.