This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
ACER3 / Alkaline ceramidase 3 · IHC design guide
Design Immunohistochemistry for ACER3
This ACER3 paraffin IHC guide uses ER/Golgi localisation as a molecular expectation (UniProt). Compare staining with high signal in placenta decidual cells (HPA tissue IHC) and optimize the catalog antibody within 1:100–1:300 (datasheet).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
ACER3 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 | ER/Golgi membranes expected; tissue compartment unreported (UniProt; HPA tissue IHC) | |
| Staining pattern | Endothelial cell staining; subcellular pattern unspecified (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Endometrium+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 across sections. (standard IHC practice; not target-specific) | |
| Caveat | Low agreement between antibody staining and RNA expression (HPA tissue IHC) | |
| Regulation | Expression regulation unreported (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope location and coverage unknown (UniProt) |
Section 1
Recommended ACER3 IHC & IF Protocols
Compare the catalog antibody's IHC-P protocol with the published mouse liver IHC method (PMC11873283: IHC methods).
| Sample | Paraffin-embedded human placenta tissue; fixative not specified (datasheet A10457-2) |
| Fixation | Image fixative and duration unreported (datasheet A10457-2); 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-ACER3, 1:100-1:300 (datasheet A10457-2) |
| 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 | ACER3-positive staining in glandular cells of endometrium (HPA tissue IHC: High). HPA tissue profile: Expressed in endothelial cells. No signal in the no-primary control. |
💡Decision noteStart with citrate pH 6.0 HIER at 95–98 °C for 20 min for membrane ACER3 (page retrieval; UniProt Q9NUN7 topology).
Section 2
What Is the Expected ACER3 Staining Pattern?
ACER3 is a 7-pass protein of the endoplasmic reticulum and Golgi membranes (UniProt Q9NUN7 topology and subcellular location). In paraffin-section IHC, assess membrane-associated cytoplasmic staining in the relevant cell population: HPA reports high staining in lung macrophages, endometrial glandular cells and several other specified cells (HPA tissue IHC). Treat the pattern as provisional because HPA rates its IHC antibody Approved but reports low consistency with RNA expression (HPA tissue IHC; HPA antibodies).
| Staining follows a cytoplasmic, often perinuclear, membrane-associated pattern in lung macrophages or endometrial glandular cells (UniProt Q9NUN7 subcellular location; HPA: High in both cell populations). | This fits the predicted ER/Golgi compartment and an HPA-observed positive population (UniProt Q9NUN7 subcellular location; HPA tissue IHC). Score the identified cells and their staining intensity; the distribution alone does not prove antibody specificity (general IHC practice). |
| Strong nuclear-only staining appears while cytoplasmic staining is absent (observed-slide scenario). | A nuclear-only pattern conflicts with ACER3's annotated ER/Golgi membrane location (UniProt Q9NUN7 subcellular location). Check a no-primary control and an HPA-observed positive cell population before interpreting that signal as ACER3 (general IHC practice; HPA tissue IHC). |
| Strong signal appears in adipocytes that were chosen as a low-signal comparator (observed-slide scenario; HPA: Not detected in adipose-tissue adipocytes). | HPA reports those adipocytes as Not detected, so strong staining there warrants a specificity or detection-background check (HPA tissue IHC; general IHC practice). HPA's Approved rating and low RNA–staining consistency limit the certainty of any tissue-based call (HPA tissue IHC). |
| Color spreads across tissue or appears in empty areas without a cell-specific pattern (observed-slide scenario). | Interpret this as background until controls establish otherwise (general IHC practice). Uneven blocking, residual detection activity or excess detection reagent can obscure a membrane-associated cytoplasmic pattern (general IHC practice; UniProt Q9NUN7 subcellular location). |
| No signal appears in lung macrophages or endometrial glandular cells (observed-slide scenario; HPA: High in both cell populations). | A negative result in an HPA-observed positive population calls for a run-level check before a biological conclusion (HPA tissue IHC; general IHC practice). Verify cell identification, tissue preservation, retrieval and detection controls; HPA staining is a reference pattern, not a guarantee for every specimen (general IHC practice; HPA tissue IHC). |
💡Expected ACER3 appearanceA persuasive positive is discernible membrane-associated cytoplasmic staining in an HPA-observed high-staining population, such as lung macrophages or endometrial glandular cells (UniProt Q9NUN7 subcellular location; HPA: High); nuclear-only color or indiscriminate background is suspect (UniProt Q9NUN7 subcellular location; general IHC practice).
| Which compartment should guide scoring? | ACER3 has 7 transmembrane segments and is annotated at ER and Golgi membranes (UniProt Q9NUN7 topology and subcellular location). Its exact antibody epitope is not supplied, so topology alone cannot set an antigen-retrieval condition (UniProt Q9NUN7 topology; evidence limitation). |
| Which cells provide useful comparators? | HPA reports High staining in lung macrophages, endometrial glandular cells, kidney glomerular cells and placental decidual cells; adipose-tissue adipocytes are Not detected (HPA tissue IHC). Choose comparators by the specified cell type within each tissue (HPA tissue IHC). |
| How firm is the tissue pattern? | The tissue-IHC reliability label is Approved, with low consistency between antibody staining and RNA expression; the listed antibody's IHC status is Approved (HPA tissue IHC; HPA antibodies). Interpret an unexpected cell pattern cautiously and review controls (general IHC practice). |
| Do variants or processing predict another pattern? | UniProt lists 2 isoforms, one chain spanning residues 1–267, and no annotated signal peptide, propeptide or glycosylation sites (UniProt Q9NUN7 isoforms, processing and glycosylation). The supplied record does not map an antibody epitope to either isoform (evidence limitation). |
| What does IF/ICC add? | HPA summarizes the ICC-IF location as Membrane but supplies no main location or cell-line images (HPA subcellular ICC-IF). That summary supports a broad membrane expectation; it cannot establish an IF staining pattern or an IF protocol (HPA subcellular ICC-IF; evidence limitation). |
| Situation | Likely cause | Next action |
|---|---|---|
| The HPA-observed positive cells are unstained (HPA: High in lung macrophages and endometrial glandular cells). | The cells may be missed during scoring, or a staining-run step may have failed (general IHC practice). | Locate the specified cells, then check the run's positive control, retrieval and detection steps (HPA tissue IHC; general IHC practice). |
| Only nuclei are stained (observed-slide scenario). | Nuclear-only signal does not match the annotated ER/Golgi membrane location (UniProt Q9NUN7 subcellular location). | Compare with a no-primary control and an HPA-observed positive population; withhold an ACER3 call if nuclear-only staining persists (general IHC practice; HPA tissue IHC). |
| Strong staining appears in adipose-tissue adipocytes (observed-slide scenario; HPA: Not detected). | The result disagrees with the HPA cell-specific reference and may reflect nonspecific staining or detection activity (HPA tissue IHC; general IHC practice). | Check no-primary and detection controls, then score adipocytes separately from neighboring cells (general IHC practice; HPA tissue IHC). |
| Background obscures cell boundaries (observed-slide scenario). | Blocking, washing or detection background may reduce readable contrast (general IHC practice). | Review the no-primary control and the blocking and wash steps; judge positive staining only where cell boundaries remain interpretable (general IHC practice). |
| A tissue appears mixed or patchy (observed-slide scenario). | HPA levels apply to named cell populations, not every cell in that tissue; its staining has low RNA consistency (HPA tissue IHC). | Score the named cells separately and record distribution alongside intensity (HPA tissue IHC; general IHC practice). |
| An IF image appears to conflict with IHC (observed-slide scenario). | HPA's ICC-IF entry reports only Membrane, without a main location or cell-line images (HPA subcellular ICC-IF). | Keep IF interpretation in its own guide and compare only the broad membrane expectation here; do not infer an IF protocol from the IHC record (HPA subcellular ICC-IF; evidence limitation). |
Experiment evidence
IHC & IF images showing ACER3 staining
A10457-2 · IHCImmunohistochemistry analysis of paraffin-embedded human placenta tissue, using PHCA Antibody. The picture on the right is blocked with the
A10457-2 · IFImmunofluorescence analysis of MCF7 cells, using PHCA Antibody. The picture on the right is blocked with the synthesized peptide.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000078124-ACER3/tissue/cerebral+cortex#imid_20444811
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000078124-ACER3/tissue/colon#imid_20444729
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000078124-ACER3/tissue/liver#imid_20444746
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000078124-ACER3/tissue/kidney#imid_20444731
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for ACER3 IHC & IF
🧪Run placenta first and expect staining in decidual cells (HPA: High in placental decidual cells; A10457-2 caption: placenta IHC). Use adipose tissue as the negative comparator (HPA: Not detected in adipocytes); on the placenta slide, compare decidual-cell staining with any neighboring cells that lack signal, without assuming those cells are biologically ACER3-negative (HPA: High in decidual cells).
Positive control tissue: Endometrium (Glandular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for ACER3; derive a cell-line control from the positive tissue's cell type (Glandular cells) and confirm it by RNA or western blot first.
Technical controls: Include no-primary (secondary-only) and isotype controls matched to the primary antibody’s host species and class, using normal host IgG if the primary is polyclonal (standard IHC practice). Use peptide blocking as a biological specificity control (A10457-2 caption: signal blocked with synthesized peptide), and quench endogenous peroxidase in placenta before chromogenic detection (standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected paraffin-section caption does not state the fixative (A10457-2 caption). Antigen-retrieval dependence is unreported, so compare retrieved and unretrieved pilot sections; the supplied evidence does not establish whether frozen sections or IF would be easier (A10457-2 caption; HPA subcellular record: no ICC-IF images). Placental endogenous peroxidase can create chromogenic background, making the secondary-only control especially useful (standard IHC practice).
HPA tissue IHC evidence for ACER3
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 |
|---|---|---|---|---|
| Endometrium | Glandular cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in glomeruli | High | Protein (IHC) | HPA → |
| Lung | Macrophages | High | Protein (IHC) | HPA → |
| Placenta | Decidual cells | High | Protein (IHC) | HPA → |
| Skin | Fibroblasts | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced ACER3 IHC Tips
Troubleshoot ACER3 staining in paraffin sections by checking retrieval, cell type and membrane associated localisation before comparing signal intensity.
Which retrieval condition should I start with for ACER3 in paraffin sections?
Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 min (page retrieval specification). Let sections cool consistently, then compare a known staining area with a no-primary control processed in the same run (standard IHC practice). ACER3 has 7 transmembrane segments and resides in endoplasmic reticulum and Golgi membranes, so assess intracellular staining rather than demanding a crisp surface outline (UniProt Q9NUN7 localisation and topology). If staining remains weak, trial a different retrieval buffer only as a fallback on adjacent sections, keeping antibody and detection conditions constant (standard IHC practice).
Could fixation explain weak ACER3 staining?
The selected antibody image shows staining in paraffin-embedded human placenta, but its caption does not report a fixative (caption: A10457-2). ACER3-specific sensitivity to fixation is therefore unknown; neither tissue staining patterns nor its 7 membrane segments establish a preferred fixation condition (HPA tissue IHC; UniProt Q9NUN7 topology). Record the fixative and processing history for each specimen, and compare sections with matched handling before attributing a difference to biology (standard IHC practice). Apply the page's citrate pH 6.0 retrieval at 95–98 °C for 20 min consistently, then assess whether morphology and staining remain interpretable (page retrieval specification; standard IHC practice).
What staining pattern fits ACER3, and when should I question it?
Expect an intracellular, membrane associated pattern compatible with endoplasmic reticulum or Golgi localisation, although chromogenic IHC alone cannot assign either organelle definitively (UniProt Q9NUN7 localisation; standard IHC practice). ACER3 spans membranes 7 times, with residues 1–33 cytoplasmic and 237–267 lumenal, so apparent staining depends partly on epitope access (UniProt Q9NUN7 topology; standard IHC practice). Assess signal within identifiable cells at high magnification and compare it with a no-primary section to check diffuse deposit (standard IHC practice). Predominantly nuclear staining warrants scrutiny because the supplied localisation is to intracellular membranes (UniProt Q9NUN7 localisation).
How do isoforms and epitope access affect an ACER3 IHC result?
ACER3 has 2 annotated isoforms, but the payload does not define their sequence differences or the catalog antibody's epitope (UniProt Q9NUN7 isoforms; supplied antibody evidence). Therefore, do not claim that this stain detects both isoforms or distinguishes them without an epitope map and independent validation (standard antibody validation practice). The protein has 7 transmembrane segments, with both cytoplasmic and lumenal regions that may differ in accessibility after processing (UniProt Q9NUN7 topology; standard IHC practice). The selected placenta image includes a synthesized-peptide block, which supports competition for staining in that image but does not establish isoform coverage (caption: A10457-2; standard antibody validation practice).
How should I assess ACER3 by multiplex IF alongside this IHC guide?
Treat IF as a separate assay: the supplied antibody image documents paraffin-section IHC in placenta, while no IF validation is supplied here (caption: A10457-2; supplied evidence). Pair ACER3 with an independently validated marker for the expected cell type, such as decidual cells in placenta, and inspect single channels before interpreting overlap (HPA: High in placenta decidual cells; standard IF practice). Choose spectrally separated fluorophores, placing a weak ACER3 signal in a channel with less tissue autofluorescence after checking an unstained control (standard IF practice). Optimise permeabilisation for an intracellular epitope; access to a lumenal region may require intracellular membrane permeabilisation, whereas a cytoplasmic region still requires access through the plasma membrane (UniProt Q9NUN7 topology; standard IF practice).
How can I separate ACER3 signal from chromogenic background?
Inspect a no-primary section for detection background and an adjacent stained section for morphology before judging faint intracellular colour as ACER3 (standard IHC practice). Include an endogenous peroxidase block when using peroxidase and DAB, and check whether pigment, tissue folds or precipitate reproduce the apparent signal (standard chromogenic IHC practice). The selected placenta image includes a synthesized-peptide-blocked comparison, but competition in that image does not exclude every source of background in other specimens (caption: A10457-2; standard antibody validation practice). Keep citrate retrieval at pH 6.0, 95–98 °C and 20 min constant while changing one blocking or detection variable at a time (page retrieval specification; standard IHC practice).
How should I quantify ACER3 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the scored cell population before measuring ACER3, since HPA reports High staining in placenta decidual cells and lung macrophages but Not detected in adipose adipocytes (HPA tissue IHC). For a cell based result, report percent positive cells and an H-score from 0–300, calculated as intensity 1–3 multiplied by the percentage at each intensity (standard IHC scoring practice). For spatially defined populations, report positive-cell density per mm² of viable tissue and state the compartment counted (standard image analysis practice). Normalise comparisons to the same cell population or viable tissue area, with identical staining and imaging settings (standard IHC quantification practice).
What would make an apparent ACER3 positive result convincing?
A convincing result shows intracellular staining in intact, identifiable cells and a cleaner matched negative control, consistent with ACER3's endoplasmic reticulum and Golgi localisation (UniProt Q9NUN7 localisation; standard IHC practice). Compare cell identity with supplied patterns, including High staining in placenta decidual cells and lung macrophages, while recognising HPA's Approved rating carries low staining–RNA consistency (HPA tissue IHC). Question predominantly nuclear deposits, tissue-edge gradients, necrotic regions and staining reproduced without primary antibody (UniProt Q9NUN7 localisation; standard IHC practice). Check endogenous peroxidase when using DAB, and treat the selected peptide-blocked placenta image as supporting evidence for that specific image rather than universal specificity (standard chromogenic IHC practice; caption: A10457-2).
Boster reagents
Best ACER3 / Alkaline ceramidase 3 IHC Antibodies
A10457-2 lists IHC and IF applications and human and mouse reactivity (catalog); its figures show paraffin-embedded human placenta IHC and MCF7-cell IF (image captions).
Real IHC data
Anti-APHC ACER3 Antibody
Cat # A10457-2
A10457-2 is listed for IHC and IF in human and mouse samples (catalog: applications and reactivity). Its IHC figure shows paraffin-embedded human placenta, and its IF figure shows MCF7 cells; both captions call the antibody “PHCA” (image captions).
Which to pick: For tissue IHC, A10457-2 has a paraffin-embedded human placenta image (IHC caption); the fixative is unreported (IHC caption). For cell IF, A10457-2 has an MCF7 image (IF caption), while ICC is not separately listed (catalog: applications). A10457-2 also lists mouse reactivity, but the supplied figures do not show mouse samples (catalog: reactivity; image captions); clonality is unreported (catalog: clone field).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9NUN7 (ACER3_HUMAN, Alkaline ceramidase 3).
- Human Protein Atlas. ACER3 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. ACER3 subcellular location (ICC-IF): Membrane.
- Human Protein Atlas. ACER3 antibody validation summary (1 antibodies).
- Targeting the ceramidase ACER3 attenuates cholestasis in mice by mitigating bile acid overload via unsaturated ceramide-mediated LXRβ signaling transduction. Nature communications 2025 — PMC11873283.
- Circular RNA circ_0001955 promotes hepatocellular carcinoma tumorigenesis by up-regulating alkaline ceramidase 3 expression through microRNA-655-3p. Bioengineered 2022 — PMC8973869.
- PubMed PMID:11356846 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:16554811 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for ACER3 (Alkaline ceramidase 3). Expected localisation ER/Golgi membranes expected; tissue compartment unreported (UniProt; HPA tissue IHC). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: A10457-2 at 1:100-1:300 (the product's own IHC validation image is shown). Controls (HPA): positive Endometrium (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human placenta tissue; fixative not specified (datasheet A10457-2); 2. Fixation: Image fixative and duration unreported (datasheet A10457-2); 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-ACER3, 1:100-1:300 (datasheet A10457-2); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Low agreement between antibody staining and RNA expression (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope location and coverage unknown (UniProt); Regulation: Expression regulation unreported (UniProt). Evidence: UniProt Q9NUN7, HPA tissue IHC · Approved, HPA ICC-IF · Membrane, Datasheet A10457-2, PMC11873283. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/ACER3/immunohistochemistry-ihc-guide.