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SNX4 / Sorting nexin-4 · IHC design guide
Design Immunohistochemistry for SNX4
Plan SNX4 staining in paraffin sections using the IHC-validated antibody, with tissue controls and chromogenic detection. Compare cytoplasmic and nuclear staining with the tissue profile while accounting for its uncertain reliability (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SNX4 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 | Tissue: cytoplasmic/nuclear (HPA tissue IHC); molecular: early endosome/ERC (UniProt) | |
| Staining pattern | Cytoplasmic and nuclear staining in several tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A08783-2) | |
| Positive control | Placenta+4 more · see all | |
| Negative control | Esophagus+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 | Tissue staining has low concordance with RNA expression (HPA tissue IHC) | |
| Regulation | Expression regulation is unannotated (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended SNX4 IHC & IF Protocols
The catalog antibody uses heat-mediated EDTA pH 8.0 retrieval (datasheet A08783-2). The published paraffin-section brain protocol below uses fluorescent detection (PMC5251330).
| Sample | Paraffin-embedded human glioblastoma tissue; fixative not specified (datasheet A08783-2) |
| Fixation | Image fixative and duration unreported (datasheet A08783-2); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet A08783-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A08783-2) |
| Primary antibody | Rabbit anti-SNX4, 2-5 μg/ml (datasheet A08783-2) |
| Primary incubation | Overnight at 4 °C (datasheet A08783-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A08783-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SNX4-positive staining in trophoblastic cells of placenta (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic and nuclear expression in several tissues. No signal in the no-primary control. |
💡Decision noteStart with EDTA pH 8.0 retrieval (datasheet A08783-2); the published brain protocol boils sections in 1 mM EDTA, pH 8.0, for 5 minutes (PMC5251330).
Section 2
What Is the Expected SNX4 Staining Pattern?
SNX4 is associated with the early endosome membrane and a juxtanuclear endocytic recycling compartment; it has no transmembrane segment (UniProt O95219 topology and subcellular location). In paraffin-section IHC, prioritize cytoplasmic staining in placental trophoblastic cells or splenic red-pulp cells, both reported as High (HPA tissue IHC). HPA also reports nuclear staining in several tissues, but rates its tissue IHC evidence Uncertain because staining and RNA expression have low consistency (HPA tissue IHC).
| Cytoplasmic staining is strongest in placental trophoblastic cells or splenic red-pulp cells (HPA tissue IHC: High in both). | This is the most useful reported positive-tissue pattern, although its specificity remains unverified (HPA tissue IHC: Uncertain). A granular or juxtanuclear emphasis would fit SNX4's annotated endosomal locations; routine chromogenic IHC may not resolve individual endosomes (UniProt O95219 subcellular location; general IHC practice). |
| Signal is predominantly nuclear, with little cytoplasmic staining (HPA tissue IHC: cytoplasmic and nuclear expression reported in several tissues). | Do not classify every nuclear signal as an artefact: HPA reports it, while UniProt places SNX4 at endosomal membranes and a juxtanuclear recycling compartment (HPA tissue IHC; UniProt O95219 subcellular location). Predominantly nuclear staining therefore needs independent specificity checks, especially given HPA's Uncertain reliability rating (HPA tissue IHC). |
| Strong staining appears in esophageal squamous epithelium or heart cardiomyocytes (HPA tissue IHC: Not detected in these cells). | That distribution conflicts with the reported tissue IHC pattern; investigate antibody cross-reactivity, endogenous chromogenic activity, or nonspecific detection before scoring it as SNX4 (HPA tissue IHC; general IHC practice). A reported Not detected result is a comparison control, not proof that every specimen or assay must be negative (HPA tissue IHC: Uncertain). |
| Broad, fairly uniform color covers tissue and the surrounding section rather than defined cells. | Interpret this as background until controls establish otherwise (general IHC practice). Examine a no-primary control for detection-system signal, then review blocking, washes, antibody concentration, and chromogen development (general IHC practice). The distribution alone cannot establish an SNX4-specific signal, particularly with an Uncertain HPA tissue IHC profile (HPA tissue IHC). |
| Placental trophoblastic cells or splenic red-pulp cells show no detectable staining (HPA tissue IHC: High in both). | First check that the section contains the expected cells and that a same-run positive control developed (general IHC practice). Review the IHC-validated antibody's documented dilution and retrieval conditions if available; none are supplied here. An absent signal may reflect assay performance, while HPA's Uncertain rating limits how firmly these tissues can define a required positive result (HPA tissue IHC). |
💡Expected SNX4 appearanceA persuasive positive is cell-associated cytoplasmic staining, potentially granular or juxtanuclear, in placental trophoblastic cells or splenic red-pulp cells reported as High (UniProt O95219 subcellular location; HPA tissue IHC), whereas broad background or strong staining in reported Not detected cell types warrants control-based review (HPA tissue IHC; general IHC practice).
| Compartment and topology | SNX4 is annotated at early endosome membranes and a juxtanuclear recycling compartment, with no transmembrane segment (UniProt O95219 topology and subcellular location). Judge cytoplasmic localization in cells, not membrane-outline staining alone; chromogenic resolution may blur small puncta (general IHC practice). |
| Tissue distribution and confidence | Placental trophoblastic cells and splenic red-pulp cells are High, while several other cell populations are Medium, Low, or Not detected (HPA tissue IHC). HPA labels the tissue IHC profile Uncertain because antibody staining and RNA data have low consistency, so use these contrasts as provisional guides (HPA tissue IHC). |
| Antibody validation | The listed antibody, HPA005709, has an Uncertain IHC validation status (HPA antibodies). Interpret unexpected compartments or cell types with controls and, when feasible, independent confirmation (general IHC practice). The supplied record gives no epitope, dilution, retrieval condition, or catalog-antibody protocol to specify here. |
| Isoform coverage | UniProt lists two SNX4 isoforms (UniProt O95219 isoforms). With no epitope information in the supplied record, coverage of both isoforms cannot be inferred; a negative stain should therefore be interpreted alongside antibody documentation and assay controls (general IHC practice). |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected positive tissue is blank (HPA tissue IHC: High in placental trophoblastic cells and splenic red-pulp cells). | The relevant cells may be absent from the section, or the staining run may have failed (general IHC practice). | Verify morphology and a same-run positive control; then check the antibody's documented IHC dilution, retrieval, and detection steps if those instructions are available (general IHC practice). |
| Signal is mainly nuclear (HPA tissue IHC: nuclear expression reported in several tissues). | The distribution is less concordant with annotated endosomal localization, though nuclear IHC staining has been reported (UniProt O95219 subcellular location; HPA tissue IHC). | Compare nuclear and cytoplasmic staining in reported positive cells, review no-primary controls, and seek independent confirmation before assigning nuclear signal to SNX4 (HPA tissue IHC: Uncertain; general IHC practice). |
| Reported Not detected cells stain strongly, such as esophageal squamous epithelium (HPA tissue IHC). | Possible antibody cross-reactivity, nonspecific binding, or endogenous detection activity (general IHC practice). | Inspect a no-primary control and assess blocking and detection chemistry; compare cell-level distribution with a reported positive tissue in the same run (HPA tissue IHC; general IHC practice). |
| Color is diffuse or persists outside cells. | Excess background can follow nonspecific detection or overly strong development (general IHC practice). | Compare no-primary and tissue controls, then adjust blocking, washes, antibody concentration, or chromogen development according to the assay instructions (general IHC practice). Do not score diffuse color as a localized SNX4 result. |
| Staining varies across tissues or between runs. | HPA reports low consistency between antibody staining and RNA expression and rates tissue IHC reliability Uncertain; technical variation may also contribute (HPA tissue IHC; general IHC practice). | Score the same cell types with matched controls and consistent processing, recording compartment, intensity, and background separately; avoid treating a single discordant section as definitive (general IHC practice). |
| IF/ICC: should SNX4 form visible endosomal puncta? | Endosomal and juxtanuclear localization is annotated, but HPA supplies no ICC-IF images or confirmed main IF location for this record (UniProt O95219 subcellular location; HPA subcellular). | Treat puncta as a localization hypothesis, not a validated IF pattern; assess antibody specificity and compare with an endosomal marker if planning the separate IF/ICC experiment (UniProt O95219 subcellular location; HPA subcellular; general IF practice). |
Experiment evidence
IHC & IF images showing SNX4 staining
A08783-2 · IHCIHC analysis of SNX4 using anti-SNX4 antibody (A08783-2). SNX4 was detected in a paraffin-embedded section of human glioblastoma tissue. Hea
A08783-2 · IHCIHC analysis of SNX4 using anti-SNX4 antibody (A08783-2). SNX4 was detected in a paraffin-embedded section of human liver cancer tissue. Hea
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000114520-SNX4/tissue/cerebral+cortex#imid_2306544
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000114520-SNX4/tissue/colon#imid_2306486
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000114520-SNX4/tissue/liver#imid_2306471
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000114520-SNX4/tissue/kidney#imid_2306472
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SNX4 IHC & IF
🧪Run placenta first and assess staining in trophoblastic cells (High; HPA: placenta), then run esophagus and assess squamous epithelial cells (Not detected; HPA: esophagus). Cells outside the trophoblastic compartment should show only control-level background on the no-primary slide; their SNX4 status is not established by the supplied HPA row (HPA: placenta).
Positive control tissue: Placenta (Trophoblastic cells, HPA High)
Negative control tissue: Esophagus (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for SNX4; derive a cell-line control from the positive tissue's cell type (Trophoblastic cells) and confirm it by RNA or western blot first.
Technical controls: Include no-primary (secondary-only) and matched rabbit IgG isotype controls, plus SNX4-knockout material or a peptide-block control if the immunizing peptide is available (selected-SKU caption: rabbit primary; standard IHC practice). For placental chromogenic sections, quench endogenous peroxidase and check for endogenous biotin if using biotin-based detection (selected-SKU caption: HRP/DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window and fixation effect are unreported; the selected-SKU paraffin-section caption does not state the fixative (selected-SKU caption: fixative not stated). Heat retrieval in EDTA at pH 8.0 was used, but retrieval dependence was not tested in the supplied evidence (selected-SKU caption: EDTA retrieval). Neither frozen-section staining nor IF ease is established here; placental blood and endogenous peroxidase can complicate chromogenic interpretation (supplied evidence: no frozen-section or IF protocol; standard IHC practice).
HPA tissue IHC evidence for SNX4
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Low consistency between antibody staining and RNA expression data. Pending external verification.). 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 |
|---|---|---|---|---|
| Placenta | Trophoblastic cells | High | Protein (IHC) | HPA → |
| Spleen | Cells in red pulp | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Medium | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Esophagus | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
| Heart muscle | Cardiomyocytes | Not detected | Protein (IHC) | HPA → |
| Lymph node | Germinal center cells | Not detected | Protein (IHC) | HPA → |
| Oral mucosa | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
| Ovary | Ovarian stroma cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SNX4 IHC Tips
Troubleshoot SNX4 staining in paraffin sections by checking retrieval, compartment, controls and scoring before interpreting chromogenic signal.
Which retrieval condition should I try first for weak SNX4 staining?
Start with heat-mediated antigen retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A08783-2). The selected SNX4 tissue image used that condition before incubation with 2 μg/ml antibody overnight at 4°C (selected IHC caption: A08783-2). If staining is weak, check that sections received consistent heating, cooling and washes before changing retrieval conditions (standard IHC practice). A different buffer or pH is a fallback to test on adjacent sections, since neither is documented for this image (selected IHC caption: A08783-2). Compare signal and tissue preservation alongside a no-primary control (standard IHC practice).
Could fixation explain inconsistent SNX4 staining between paraffin blocks?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative (selected IHC caption: fixative not stated). Record each block’s fixation and processing history before comparing staining intensity, since those steps can alter antigen accessibility in IHC (standard IHC practice). Stain adjacent sections from each block with the same pH 8.0 EDTA retrieval and detection run to limit processing differences (datasheet A08783-2; standard IHC practice). Include tissue and no-primary controls in that run to identify technical variation (standard IHC practice). Do not assign a block-to-block difference to SNX4 biology until those controls are consistent (standard IHC practice).
Where should convincing SNX4 signal appear in a tissue section?
Look for intracellular, often punctate or juxtanuclear staining consistent with an early endosome membrane and endocytic recycling compartment (UniProt O95219: subcellular location; standard IHC interpretation). SNX4 has no transmembrane segment, so a crisp cell-surface outline alone would be an unexpected pattern (UniProt O95219: topology). The tissue atlas reports cytoplasmic and nuclear staining across several tissues, but rates its IHC reliability uncertain because staining and RNA expression show low consistency (HPA: tissue IHC). Evaluate the pattern within identified cells using morphology and a matched control section (standard IHC practice). Treat isolated nuclear staining cautiously until an independent control supports it (HPA: uncertain reliability; standard IHC practice).
How can an unknown antibody epitope affect interpretation of SNX4 IHC?
SNX4 has 2 annotated isoforms, and its PX domain spans residues 61–187 (UniProt O95219: isoforms and domains). The supplied antibody caption does not identify its binding epitope, so staining cannot be assigned to one isoform from this IHC result alone (selected IHC caption: A08783-2; UniProt O95219: isoforms). Check the antibody’s documented immunogen or epitope before comparing specimens that might express different isoforms (standard IHC practice). Keep retrieval and antibody concentration constant during that comparison; the illustrated condition used 2 μg/ml overnight at 4°C (selected IHC caption: A08783-2). Interpret a negative compartment as an accessibility question as well as a possible biological result (standard IHC practice).
How should I follow up a chromogenic SNX4 result with multiplex IF?
Treat multiplex IF as a separate optimisation from this paraffin-section IHC result; the supplied tissue image documents chromogenic detection only (selected IHC caption: A08783-2). Pair SNX4 with a marker identifying the cell population under study, and inspect whether puncta occur within those marker-positive cells (standard IF practice; UniProt O95219: early endosome location). Choose spectrally separated fluorophores after checking tissue autofluorescence in unstained sections, with preference for the cleaner channel for weak signal (standard IF practice). Test permeabilisation because the expected signal is intracellular, while the antibody’s epitope and accessibility are unspecified (UniProt O95219: subcellular location; selected IHC caption: A08783-2). Include single-stain and no-primary controls to assess bleed-through and background (standard IF practice).
What should I change if SNX4 DAB staining is diffuse?
First inspect a no-primary section for detection-system signal and a matched stained section for tissue-edge or necrotic staining (standard IHC practice). The illustrated workflow used 10% goat serum, an anti-rabbit secondary for 30 minutes at 37°C, and DAB development (selected IHC caption: A08783-2). Use an appropriate endogenous-peroxidase block before detection, then compare shorter chromogen development and stronger washing on adjacent sections (standard IHC practice). Titrate the primary around the illustrated 2 μg/ml condition if diffuse staining persists (selected IHC caption: A08783-2; standard IHC practice). Retain punctate intracellular staining only when it exceeds control background and preserves tissue morphology (UniProt O95219: subcellular location; standard IHC practice).
How can I score SNX4 staining reproducibly across sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, and use the same retrieval, detection and exposure to DAB across compared sections (standard IHC practice). An H-score combines the percentage of cells at each intensity grade into a 0–300 score; alternatively, report percent-positive cells or positive puncta density per mm² (standard IHC quantification practice). Normalise counts to the area or number of viable cells in the prespecified compartment, excluding necrosis and tissue edges (standard IHC practice). Record cytoplasmic or juxtanuclear and nuclear staining separately because the expected trafficking location and reported tissue pattern differ (UniProt O95219: subcellular location; HPA: tissue IHC). Apply one threshold across batches using controls (standard IHC practice).
How do I distinguish true SNX4 staining from artefact?
Give greatest weight to reproducible intracellular puncta or juxtanuclear signal in intact cells, consistent with SNX4’s endosomal and recycling-compartment locations (UniProt O95219: subcellular location; standard IHC interpretation). Check cell identity before interpreting a tissue-wide pattern: trophoblastic cells in placenta and red-pulp cells in spleen have reported high staining, but atlas IHC reliability is uncertain (HPA: tissue IHC). Diffuse staining confined to edges or necrosis, or signal reproduced without primary antibody, suggests artefact (standard IHC practice). Endogenous enzyme activity can also produce chromogenic signal, so assess a peroxidase-block control when needed (standard IHC practice). Do not treat nuclear staining alone as confirmation of SNX4 (HPA: uncertain reliability; UniProt O95219: subcellular location).
Boster reagents
Best SNX4 / Sorting nexin-4 IHC Antibodies
A08783-2 has real IHC data from human paraffin sections; no IF/ICC data are supplied (catalog IHC captions; catalog applications and images).
Real IHC data
Anti-SNX4 Antibody ®
Cat # A08783-2
A08783-2 has IHC images from human paraffin sections of glioblastoma, liver cancer, thyroid papillary carcinoma, and colon adenocarcinoma (catalog IHC captions). Human, mouse, and rat reactivity is listed, while the IHC dilution applies to human samples (catalog reactivity and dilution).
Which to pick: Choose A08783-2 for human paraffin-section chromogenic IHC: its own glioblastoma image shows EDTA pH 8 retrieval, 2 μg/ml rabbit primary antibody, and HRP/DAB detection; the fixative is unreported (A08783-2 IHC caption). No IF/ICC-validated SKU is provided, and clonality is unreported (catalog applications, images, and clone field). A08783-2 lists mouse and rat reactivity, but the supplied paraffin-section IHC images and 2–5 μg/ml IHC recommendation cover human samples (catalog reactivity and dilution; A08783-2 IHC captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry O95219 (SNX4_HUMAN, Sorting nexin-4).
- Human Protein Atlas. SNX4 tissue IHC expression (reliability: Uncertain).
- Human Protein Atlas. SNX4 subcellular location (ICC-IF): Highest expression in SH-SY5Y: 47.9 nTPM.
- Human Protein Atlas. SNX4 antibody validation summary (1 antibodies).
- Sorting nexin-4 regulates β-amyloid production by modulating β-site-activating cleavage enzyme-1. Alzheimer's research & therapy 2017 — PMC5251330.
- PubMed PMID:9819414 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:16641997 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SNX4 (Sorting nexin-4). Expected localisation Tissue: cytoplasmic/nuclear (HPA tissue IHC); molecular: early endosome/ERC (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A08783-2). Validated IHC antibody: A08783-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Placenta (Trophoblastic cells); negative Esophagus. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human glioblastoma tissue; fixative not specified (datasheet A08783-2); 2. Fixation: Image fixative and duration unreported (datasheet A08783-2); 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 retrieval: EDTA pH 8.0 (datasheet A08783-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A08783-2); 8. Primary antibody: Rabbit anti-SNX4, 2-5 μg/ml (datasheet A08783-2); 9. Primary incubation: Overnight at 4 °C (datasheet A08783-2). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Tissue staining has low concordance with RNA expression (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope coverage is unspecified (UniProt); Regulation: Expression regulation is unannotated (UniProt). Evidence: UniProt O95219, HPA tissue IHC · Uncertain, HPA cell-line RNA · Highest expression in SH-SY5Y: 47.9 nTPM, Datasheet A08783-2, PMC5251330. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SNX4/immunohistochemistry-ihc-guide.