APAF1 / Apoptotic protease-activating factor 1 · IHC design guide

Design Immunohistochemistry for APAF1

Plan APAF1 staining in paraffin sections around its expected cytoplasmic location (UniProt) and the tissue IHC pattern, which is most abundant in immune cell subsets (HPA tissue IHC). Use bone marrow hematopoietic cells as a positive reference (HPA tissue IHC), and check antibody epitope coverage across the six isoforms (UniProt).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for APAF1 (IHC for APAF1): expected localisation Cytoplasm expected; cytoplasmic tissue staining observed (UniProt; HPA tissue IHC), antibody A00889, validated IHC image, and IHC protocol steps
Printable APAF1 IHC protocol sheet — expected localisation Cytoplasm expected; cytoplasmic tissue staining observed (UniProt; HPA tissue IHC), antibody A00889, controls and protocol steps. Open the full APAF1 IHC guide →

APAF1 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 Cytoplasm expected; cytoplasmic tissue staining observed (UniProt; HPA tissue IHC)
Staining pattern General cytoplasmic stain, most abundant in immune cell subsets (HPA tissue IHC)
Antigen retrieval Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen)
Positive control ⓘ Bone marrow+4 more · see all
Negative control ⓘ Adipose tissue+4 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep fixation consistent (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A00889)
Caveat Marrow endogenous peroxidase can mimic chromogenic signal (HPA tissue IHC; standard IHC practice)
Regulation Stimulus-dependent regulation is unreported (UniProt)
Isoform / epitope 6 isoforms; verify that the antibody epitope is shared (UniProt)
Section 1

Recommended APAF1 IHC & IF Protocols

The catalog antibody protocol is followed by published APAF1 IHC methods for solitary fibrous tumor, pancreatic ductal adenocarcinoma, and mouse lung (PMC6746689; PMC4775273; PMC6892980).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleTissue sections; selected-image fixative not specified (standard IHC workflow)
FixationImage fixative and duration unreported (datasheet A00889); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibodyRabbit anti-APAF1, 1 μg/mL (datasheet A00889)
Primary incubationOvernight at 4 °C (standard)
DetectionHRP-polymer secondary, DAB chromogen 5–10 min (standard)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultAPAF1-positive staining in hematopoietic cells of bone marrow (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression, most abundant in subsets of immune cells. No signal in the no-primary control.
💡Decision noteStart with citrate pH 6.0 retrieval at 95–98 °C for 20 min (page retrieval guidance); the pancreatic study used 98 °C for 20 min (PMC4775273).
Section 2

What Is the Expected APAF1 Staining Pattern?

APAF1 is a cytoplasmic protein with no transmembrane segment (UniProt O14727 localization and topology). In paraffin sections, expect cytoplasmic staining, strongest in bone marrow hematopoietic cells; several glandular and endothelial populations show medium staining (HPA tissue IHC). HPA describes general cytoplasmic expression, most abundant in subsets of immune cells, but rates agreement between staining and RNA as medium (HPA tissue IHC: Enhanced reliability description).

What am I looking at on my slide?
Bone marrow hematopoietic cells show clear cytoplasmic chromogenic staining.This is the strongest listed tissue pattern: HPA scores these cells High (HPA tissue IHC: bone marrow). Assess staining within the hematopoietic cells rather than calling an entire marrow section uniformly positive; the HPA profile emphasizes subsets of immune cells (HPA tissue IHC profile).
Appendix or duodenal glandular cells, or colon endothelial cells, show moderate cytoplasmic staining.These are plausible positives: each named cell population is scored Medium (HPA tissue IHC: appendix, duodenum, colon). Their lower reported intensity makes them less decisive than High bone marrow hematopoietic cells when judging a weak run (HPA tissue IHC: bone marrow).
A section shows predominantly nuclear staining with little cytoplasmic signal.For tissue IHC, this departs from HPA's general cytoplasmic profile and UniProt's cytoplasmic assignment (HPA tissue IHC profile; UniProt O14727 localization). Review morphology and controls before calling it APAF1. HPA separately reports nucleoplasm in ICC-IF, so nuclear signal alone is not universal proof of artefact (HPA subcellular ICC-IF).
Cells reported as Not detected stain strongly, such as adipocytes or heart muscle cardiomyocytes.That pattern conflicts with the cited tissue observations (HPA tissue IHC: adipocytes and cardiomyocytes, Not detected). Consider cross-reactivity or endogenous chromogenic activity, then compare a matched negative control and the expected cellular compartment (general IHC practice; UniProt O14727 localization). A conflicting cell is a warning, not proof of either cause.
Color spreads across extracellular spaces or broadly obscures cell boundaries.This is background rather than an interpretable cytoplasmic cell pattern (general IHC interpretation; HPA tissue IHC profile). Compare the negative control, counterstain and cell morphology before scoring. Diffuse staining confined to identifiable cytoplasm can still fit the reported APAF1 localization (UniProt O14727 localization).
💡Expected APAF1 appearanceCall a section positive when identifiable bone marrow hematopoietic cells show strong cytoplasmic signal, or listed glandular or endothelial cells show moderate cytoplasmic signal (HPA tissue IHC: High and Medium; UniProt O14727 localization); broad extracellular color or staining confined to HPA Not detected cell populations is suspect (general IHC interpretation; HPA tissue IHC: Not detected).
How each factor affects the staining
Tissue and cell populationAPAF1 is broadly expressed at the tissue level (UniProt O14727 tissue specificity), yet HPA staining varies by annotated cell type: High in bone marrow hematopoietic cells, Medium in selected glandular and endothelial cells, and Not detected in several listed populations (HPA tissue IHC). Select and score the actual cell population.
Evidence and antibody validationThe tissue profile carries Enhanced reliability with medium staining–RNA consistency, and HPA cautions that some stained cells or structures are unannotated (HPA tissue IHC reliability description). HPA031373 has Enhanced IHC validation; CAB069399 has Approved IHC validation (HPA antibody validation). These labels support interpretation of observed patterns without guaranteeing every antibody preparation.
Isoforms and processingUniProt lists six APAF1 isoforms and a single 1–1248 chain, with no signal peptide or propeptide (UniProt O14727 isoforms and processing). Isoform 6 is less effective at inducing apoptosis (UniProt O14727 function). Without an antibody epitope in the payload, staining cannot identify an isoform or establish its apoptotic activity.
What should IF/ICC show?HPA reports mainly nucleoplasm and cytosol, with additional Golgi localization, in ICC-IF images from A-431, U-251MG and U2OS (HPA subcellular ICC-IF). This is a separate cell-imaging observation from the cytoplasmic tissue IHC profile; HPA031373 has Uncertain ICC validation (HPA antibody validation).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
No signal in bone marrow hematopoietic cells.The result conflicts with a High HPA observation, though HPA notes only medium staining–RNA consistency (HPA tissue IHC: bone marrow and reliability description).Confirm that hematopoietic cells are present and identifiable. Check the assay's positive control, detection reagents and the IHC-validated antibody's documented retrieval and dilution settings (general IHC practice); no APAF1-specific fixation sensitivity is reported here.
Strong signal appears only in nuclei on tissue IHC.The pattern differs from cytoplasmic tissue expression (HPA tissue IHC profile; UniProt O14727 localization). ICC-IF nucleoplasmic staining alone does not validate a nuclear-only tissue result (HPA subcellular ICC-IF).Inspect cellular boundaries and counterstain, then compare positive and negative controls before assigning compartment or specificity (general IHC practice).
Strong staining appears in adipocytes or cardiomyocytes.Those cell populations are listed as Not detected, so the result needs verification (HPA tissue IHC: adipose tissue and heart muscle). Cross-reactivity or endogenous detection activity are possible explanations (general IHC practice).Check the stained cell identity and cytoplasmic distribution. Use a matched negative control and, for an enzyme-based chromogen, review the appropriate endogenous activity block (general IHC practice).
Diffuse color obscures most of the section.Unresolved background prevents cell-level interpretation (general IHC practice); HPA describes a cytoplasmic pattern concentrated in immune-cell subsets (HPA tissue IHC profile).Compare a negative control and review blocking, antibody concentration, washes and detection development under the assay's standard conditions (general IHC practice). Score only cells whose boundaries remain clear.
Only faint signal appears in a listed Medium population.A Medium HPA observation can be harder to distinguish from background than the High bone marrow observation (HPA tissue IHC: appendix, duodenum, colon and bone marrow).Check a bone marrow positive control if available, verify that the listed cell type is present, and assess signal against its local background before changing the assay (general IHC practice; HPA tissue IHC: bone marrow).
A granular or perinuclear focus is treated as the sole tissue-IHC positive pattern.HPA's additional Golgi location comes from ICC-IF, while its tissue IHC summary describes general cytoplasmic expression (HPA subcellular ICC-IF; HPA tissue IHC profile).Reassess the entire cytoplasm and compare cell-level staining with an appropriate positive tissue and negative control. Keep the ICC-IF location as context, not a tissue-IHC scoring rule (general IHC interpretation; HPA tissue IHC profile).

Sample controls for APAF1 IHC & IF

🧪Run bone marrow first: hematopoietic cells should stain (HPA: High in bone marrow hematopoietic cells). Use adipose tissue as the negative tissue, where adipocytes are not detected (HPA: adipose adipocytes Not detected); cells without specific staining on the bone marrow slide should show only background, without assigning a negative cell type that HPA does not identify.
Positive control tissue: Bone marrow (Hematopoietic cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show APAF1 in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (approved), Cytosol (supported) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) control, an isotype control matched to the primary antibody’s host species and immunoglobulin class, and a biological specificity control using knockout material or peptide blocking when suitable (standard IHC practice). Quench endogenous peroxidase and compare background with the controls in bone marrow, particularly around hematopoietic cells (HPA: High in bone marrow hematopoietic cells; standard IHC practice).
⚠️Feasibility: A target-specific fixation window and antigen-retrieval dependence are unreported in the supplied evidence; the A00889 human-heart IHC caption specifies 1 µg/mL but does not report a fixative (selected A00889 IHC caption). The supplied evidence does not establish that frozen sections or IF are easier than paraffin IHC for APAF1 (selected A00889 IHC caption; HPA subcellular). In bone marrow, endogenous peroxidase can produce chromogenic background and should be assessed with the controls (HPA: High in bone marrow hematopoietic cells; standard IHC practice).

HPA tissue IHC evidence for APAF1

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data. Antibody staining in cells/structures not annotated, view images.). 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
Bone marrow Hematopoietic cells High Protein (IHC) HPA →
Appendix Glandular cells Medium Protein (IHC) HPA →
Colon Endothelial cells Medium Protein (IHC) HPA →
Duodenum Glandular cells Medium Protein (IHC) HPA →
Endometrium Glandular cells Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes Not detected Protein (IHC) HPA →
Adrenal gland Glandular cells Not detected Protein (IHC) HPA →
Cerebellum Cells in granular layer Not detected Protein (IHC) HPA →
Cervix Glandular cells Not detected Protein (IHC) HPA →
Esophagus Squamous epithelial cells Not detected Protein (IHC) HPA →
Section 3

Advanced APAF1 IHC Tips

Troubleshoot APAF1 staining in chromogenic paraffin section IHC using compartment, cell type and protocol controls; the IF/ICC entry addresses the separate fluorescence workflow.

How should I adjust retrieval when APAF1 staining is weak or uneven?
Begin with citrate pH 6.0 HIER at 95–98 °C for 20 min (page protocol: APAF1 retrieval). APAF1 lacks a transmembrane segment and is annotated in the cytoplasm, so assess intracellular staining after retrieval (UniProt O14727: topology and subcellular location). If signal is weak, compare a modestly longer retrieval against the stated condition on adjacent sections, while keeping antibody concentration and detection constant (standard IHC practice). Record tissue loss and edge accentuation as well as signal, since excessive heat can compromise section morphology (standard IHC practice). Use the same retrieval condition for positive and negative controls before comparing staining intensity (standard IHC practice).
Could fixation explain inconsistent APAF1 staining across paraffin blocks?
Target-specific APAF1 fixation sensitivity is unknown from the supplied evidence; the human heart IHC caption reports 1 µg/mL antibody but no fixative or fixation duration (selected A00889 IHC caption). For a new paraffin series, document fixative, fixation duration, section age and processing alongside each block (standard IHC practice). Compare adjacent sections from similarly processed blocks before changing retrieval or antibody concentration, because those changes can obscure a processing difference (standard IHC practice). Include an on-slide positive control and inspect morphology when staining varies across a run (standard IHC practice). Do not infer a fixation effect from tissue expression patterns or protein topology (HPA: tissue IHC profile; UniProt O14727: topology).
Where should convincing APAF1 signal appear in tissue sections?
Start by evaluating cytoplasmic signal, consistent with APAF1's cytoplasmic annotation and absence of a transmembrane segment (UniProt O14727: subcellular location and topology). Tissue IHC reports general cytoplasmic expression, most abundant in subsets of immune cells, with high staining in bone marrow hematopoietic cells (HPA: tissue IHC profile; HPA: High in bone marrow hematopoietic cells). A separate cell imaging record also reports nucleoplasm and cytosol, with additional Golgi localisation; it does not establish that every tissue compartment must stain (HPA: subcellular summary). Compare cell identity and compartment against matched controls before interpreting isolated nuclear, surface or extracellular chromogen as APAF1 (standard IHC practice; UniProt O14727: topology).
How might APAF1 isoforms or epitope placement affect IHC results?
APAF1 has 6 annotated isoforms, but the supplied antibody evidence does not map the A00889 epitope or establish isoform coverage (UniProt O14727: isoforms; selected A00889 IHC caption). The annotated CARD spans residues 1–90 and NB-ARC spans 104–415, making epitope position relevant when interpreting an isoform-sensitive result (UniProt O14727: domains). Request an epitope map or compare independently validated antibodies if staining differs from an orthogonal expression measure (standard IHC practice). Keep retrieval and detection conditions matched when comparing antibodies, and report their epitopes and isoform coverage only when documented (standard IHC practice). Staining alone cannot assign a particular APAF1 isoform (UniProt O14727: isoforms).
How should I assess APAF1 by IF alongside the chromogenic IHC findings?
Treat IF/ICC as a separate assay: the selected A00889 caption documents tissue IHC, while the supplied IF localisation record comes from cell images (selected A00889 IHC caption; HPA: subcellular record). Multiplex APAF1 with a validated hematopoietic cell marker when examining bone marrow, where hematopoietic cells have high tissue staining (HPA: High in bone marrow hematopoietic cells; standard IF practice). Choose a fluorophore after checking tissue autofluorescence and include single-stain and secondary-only controls (standard IF practice). Because APAF1 has no transmembrane segment and is annotated in the cytoplasm, use a permeabilisation condition that admits antibody to intracellular epitopes (UniProt O14727: topology and subcellular location; standard IF practice). Optimise fixation and permeabilisation directly for IF rather than transferring unreported IHC processing conditions (standard IF practice; selected A00889 IHC caption).
What should I check when APAF1 chromogen appears widespread or granular?
Compare the staining pattern with the expected cytoplasmic tissue profile before increasing antibody stringency (HPA: tissue IHC profile). Run a no-primary control to reveal secondary reagent or detection background, and apply a peroxidase block before DAB when using an HRP system (standard IHC practice). In blood-rich or inflammatory areas, check whether brown signal tracks endogenous enzyme activity or pigment rather than cell cytoplasm (standard IHC practice). Titrate antibody and detection exposure on adjacent sections while retaining a documented positive control; the selected heart image used 1 µg/mL, which is evidence for that image only (selected A00889 IHC caption; standard IHC practice). Record edge and necrotic staining separately from intact-cell signal (standard IHC practice).
How can I quantify APAF1 IHC across samples with different cell compositions? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, because tissue IHC describes general cytoplasmic expression with stronger staining in subsets of immune cells (HPA: tissue IHC profile). For intact target cells, record percent positive and an H-score using intensity grades 0–3 across all scored cells; state the positivity threshold (standard IHC practice). If the question concerns infiltrating cells, report positive-cell density per mm² and the fraction positive within the relevant cell population (standard IHC practice). Normalise comparisons to the number of eligible cells or analysed tissue area, and exclude necrosis and section edges consistently (standard IHC practice). Keep retrieval, imaging and scoring thresholds fixed across batches (standard IHC practice).
How do I distinguish genuine APAF1 staining from a misleading positive result?
Favour reproducible intracellular staining in morphologically intact cells, especially cytoplasmic signal compatible with tissue IHC and UniProt localisation (HPA: tissue IHC profile; UniProt O14727: subcellular location). Use cell identity carefully: bone marrow hematopoietic cells stain high, whereas HPA did not detect APAF1 in heart muscle cardiomyocytes (HPA: High in bone marrow hematopoietic cells; HPA: Not detected in heart muscle cardiomyocytes). The selected antibody's human heart image shows tissue IHC at 1 µg/mL, but its caption does not identify positive cell types or fixation (selected A00889 IHC caption). Reject edge-only, necrotic, extracellular or no-primary-positive chromogen as evidence without further controls (standard IHC practice). APAF1 presence alone does not establish apoptosome assembly or active apoptosis (UniProt O14727: subunit and function).
Boster reagents

Best APAF1 / Apoptotic protease-activating factor 1 IHC Antibodies

Three APAF1 antibodies have IHC images from human heart tissue (A00889 caption), paraffin-embedded mouse kidney (M00889 caption), and K562 cells (M00889-2 caption); A00889 also has a K562 IF image (A00889 caption).

Real IHC data Immunohistochemistry of Apaf1 in human heart tissue with Apaf1 antibody at 1 μg/mL.
Anti-Apaf1 Antibody
Cat # A00889
Real IHC data Immunohistochemical analysis of paraffin-embedded mouse kidney, using APAF1 Antibody .
Anti-APAF1 Rabbit Monoclonal Antibody
Cat # M00889
Real IHC data Immunohistochemistry of Apaf1 in K562 cells with Apaf1 antibody at 0.5 μg/mL.
Anti-Apaf-1 Monoclonal Antibody [2E10]
Cat # M00889-2

A00889 shows IHC in human heart tissue and IF in K562 cells (A00889 image captions); M00889 shows IHC in paraffin-embedded mouse kidney (M00889 IHC caption). M00889-2 shows IHC in K562 cells (M00889-2 IHC caption); all three list Human reactivity (catalog reactivity).

Which to pick: For paraffin-section tissue IHC, choose M00889: its mouse-kidney image specifies paraffin embedding, but the fixative is unreported (M00889 IHC caption). For IF with image evidence, choose A00889 (A00889 IF caption); for ICC, M00889 lists ICC/IF and is a rabbit monoclonal (M00889 catalog applications/clone). For cross-species IHC, A00889 and mouse monoclonal M00889-2 list Human, Mouse, and Rat reactivity (catalog reactivity/host/clone); their IHC images show human heart tissue and K562 cells, respectively (A00889 and M00889-2 IHC captions).

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

References

  1. UniProt Consortium. UniProt entry O14727 (APAF_HUMAN, Apoptotic protease-activating factor 1).
  2. Human Protein Atlas. APAF1 tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. APAF1 subcellular location (ICC-IF): Mainly localized to the nucleoplasm and cytosol. In addition localized to the Golgi apparatus..
  4. Human Protein Atlas. APAF1 antibody validation summary (2 antibodies).
  5. Molecular changes in solitary fibrous tumor progression. Journal of molecular medicine (Berlin, Germany) 2019 — PMC6746689.
  6. Apoptosome-dependent caspase activation proteins as prognostic markers in Stage II and III colorectal cancer. British journal of cancer 2012 — PMC3341858.
  7. Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma. Nature medicine 2015 — PMC4775273.
  8. Pulmonary Exposure to Magnéli Phase Titanium Suboxides Results in Significant Macrophage Abnormalities and Decreased Lung Function. Frontiers in immunology 2019 — PMC6892980.
  9. PubMed PMID:9267021 — UniProt-cited evidence.
  10. PubMed PMID:10441496 — UniProt-cited evidence.
  11. PubMed PMID:10364241 — UniProt-cited evidence.