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CDH3 / Cadherin-3 · IHC design guide
Design Immunohistochemistry for CDH3
Plan chromogenic IHC on paraffin sections with catalog antibody PA1363 at 0.5–1 μg/mL (datasheet). Assess membranous staining in squamous epithelia (HPA tissue IHC), using high-staining placental cytotrophoblasts or skin basal-layer cells as positive controls (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CDH3 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 | Cell membrane (UniProt) | |
| Staining pattern | Membranous staining in squamous epithelial cells (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet PA1363) | |
| Positive control | Bronchus+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image PA1363) | |
| Caveat | Skin staining may favor basal-layer cells (HPA tissue IHC) | |
| Regulation | Expression varies across tissues (HPA tissue IHC) | |
| Isoform / epitope | 2 isoforms; extracellular vs cytoplasmic epitope matters (UniProt) |
Section 1
Recommended CDH3 IHC & IF Protocols
Use the catalog antibody’s IHC-P protocol (datasheet: PA1363) alongside these 4 published CDH3 protocols (PMC10670999; PMC5058855; PMC11951682; PMC5325383).
| Sample | Paraffin-embedded human placenta tissues; fixative not specified (datasheet PA1363) |
| Fixation | Image fixative and duration unreported (datasheet PA1363); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet PA1363) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PA1363) |
| Primary antibody | Rabbit anti-CDH3, 0.5-1μg/ml (datasheet PA1363) |
| Primary incubation | Overnight at 4 °C (datasheet PA1363) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PA1363) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CDH3-positive staining in respiratory epithelial cells of bronchus (HPA tissue IHC: High). HPA tissue profile: Membranous expression in squamous epithelia. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated citrate retrieval at pH 6 (datasheet: PA1363); the colorectal tissue microarray protocol also used citrate at pH 6 (PMC11951682).
Section 2
What Is the Expected CDH3 Staining Pattern?
CDH3 is a cell membrane cadherin with an extracellular region at residues 108–654 and a cytoplasmic region at 678–829 (UniProt P22223 topology). Expect membranous staining in selected epithelial cells, especially squamous epithelia, and in placental cytotrophoblasts (HPA tissue IHC). HPA rates the tissue IHC profile Enhanced, while reporting medium consistency between antibody staining and RNA expression (HPA tissue IHC).
| Distinct staining outlines squamous epithelial cells, especially in oral mucosa or tonsil (HPA tissue IHC). | This fits CDH3 at the cell membrane (UniProt P22223 topology; HPA tissue IHC). HPA reports High staining in those cell populations; judge the outlined cells rather than the section's overall color. |
| Strong nuclear staining, or cytoplasmic staining that dominates over cell borders, appears in an otherwise positive epithelium. | That is discordant with the reported cell membrane pattern (UniProt P22223 topology; HPA tissue IHC). Treat it as a possible artefact and review localization and staining controls before scoring it as CDH3. |
| Adipocytes or bone marrow hematopoietic cells stain, despite their Not detected HPA entries (HPA tissue IHC). | Consider cross-reactivity or endogenous detection activity (standard IHC practice). The HPA entries describe those specific cell populations; they do not establish that every cell in either tissue must be negative. |
| Diffuse chromogen covers cells and spaces without reproducible cell border definition. | Diffuse background cannot establish the membrane localization expected for CDH3 (UniProt P22223 topology; HPA tissue IHC). Check blocking, detection background, washing, and the negative control (standard IHC practice). |
| No signal appears in a correctly identified oral mucosa squamous epithelium or placental cytotrophoblast control. | Both populations have High HPA staining (HPA tissue IHC). Check control integrity and the IHC detection workflow before interpreting an unstained test section as CDH3 negative (standard IHC practice). |
💡Expected CDH3 appearanceCall positive when clear cell border staining marks the appropriate epithelium, with High staining expected in oral mucosa squamous cells, skin basal layer cells, or placental cytotrophoblasts (HPA tissue IHC); isolated nuclear color or staining of HPA Not detected adipocytes is suspect (UniProt P22223 topology; HPA tissue IHC).
| Cell population and tissue choice | HPA reports High staining in bronchial and nasopharyngeal respiratory epithelium, oral mucosa and tonsil squamous epithelium, skin basal layer cells, and placental cytotrophoblasts (HPA tissue IHC). Breast glandular and cervical squamous cells are Medium (HPA tissue IHC). |
| Reported negative cells | HPA lists adipocytes, bone marrow hematopoietic cells, and duodenal glandular cells as Not detected (HPA tissue IHC). Interpret these as cell specific reference patterns, since an unstained named population cannot validate every cell in the same section. |
| Topology and antigen location | The mature CDH3 chain spans residues 108–829; residues 108–654 are extracellular and 678–829 cytoplasmic (UniProt P22223 topology and processing). Antibody epitope location is unspecified here, so this record cannot predict an epitope specific retrieval response. |
| Processing, glycosylation, and isoforms | UniProt records a signal peptide at 1–24, propeptide at 25–107, glycosylation sites at 200 and 566, and two isoforms (UniProt P22223). These facts alone do not establish shedding, differential IHC staining, or fixation sensitivity. |
| How much confidence to place in a pattern | HPA labels the tissue IHC profile Enhanced but describes antibody staining versus RNA expression as medium consistency (HPA tissue IHC). Its antibody entries also give Enhanced IHC status to HPA001767 and CAB002487 (HPA antibodies). |
| IF/ICC Q: Where should CDH3 fluorescence appear? | A: At the plasma membrane and cell junctions, both supported HPA locations (HPA subcellular ICC-IF). This localization supports the compartment check; use the separate IF/ICC guide for its workflow. |
| Situation | Likely cause | Next action |
|---|---|---|
| A known High control has no visible membrane signal. | The run may have failed at tissue identification, antigen retrieval, primary antibody application, or detection (standard IHC practice). | Confirm the named positive cells, then check each IHC step and a run control (standard IHC practice). HPA High is an observed pattern, not proof of a fixation specific failure (HPA tissue IHC). |
| Expected borders are faint in breast glandular or cervical squamous cells. | Both populations are reported at Medium rather than High staining (HPA tissue IHC). | Compare with a High control such as oral mucosa squamous epithelium before changing interpretation (HPA tissue IHC). Score visible borders in the named cells, not overall tissue darkness (standard IHC practice). |
| The whole section has diffuse brown haze. | Nonspecific background or endogenous detection activity may obscure cell borders (standard IHC practice). | Review blocking, washes, chromogen exposure, and a negative control (standard IHC practice). Require membrane localization before assigning CDH3 positivity (UniProt P22223 topology; HPA tissue IHC). |
| Nuclei or cytoplasm stain more strongly than junctional borders. | The compartment conflicts with reported membrane localization (UniProt P22223 topology; HPA tissue IHC); the observation alone does not identify the technical cause. | Check a positive control for border staining and examine detection background (standard IHC practice). Do not score nuclear only color as the expected CDH3 pattern. |
| Adipocytes or marrow hematopoietic cells appear positive. | Those named populations are Not detected in HPA tissue IHC; cross-reactivity or endogenous detection activity is possible (HPA tissue IHC; standard IHC practice). | Compare a negative control and a membrane positive epithelial control (standard IHC practice; HPA tissue IHC). Resolve the unexpected signal before calling these cells CDH3 positive. |
| A low level glandular population is called negative after comparison with a High epithelial control. | HPA reports Low staining in thyroid, salivary, stomach, gallbladder, seminal vesicle, and prostate glandular cells (HPA tissue IHC). | Assess the named glandular cells at appropriate magnification and record whether cell border signal is detectable (standard IHC practice). Avoid applying a High control's intensity threshold to an HPA Low population. |
Experiment evidence
IHC & IF images showing CDH3 staining
PA1363 · IHCIHC analysis of CDH3 using anti-CDH3 antibody (PA1363). CDH3 was detected in paraffin-embedded section of human placenta tissues. Heat media
PA1363 · IHCIHC analysis of CDH3 using anti-CDH3 antibody (PA1363). CDH3 was detected in immunocytochemical section of A549 cell. Enzyme antigen retriev
A03353-1 · IFIF analysis of P cadherin/CDH3 using anti-P cadherin/CDH3 antibody (A03353-1). P cadherin/CDH3 was detected in immunocytochemical section of
M03353 · IFIF analysis of P cadherin using anti-P cadherin antibody (M03353). P cadherin was detected in immunocytochemical section of A431 cells. Enzy
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000062038-CDH3/tissue/cerebral+cortex#imid_993656
HPA · Oral mucosaHuman Protein Atlas IHC, Oral mucosa. Source: https://www.proteinatlas.org/ENSG00000062038-CDH3/tissue/oral+mucosa#imid_993580
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000062038-CDH3/tissue/colon#imid_993582
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000062038-CDH3/tissue/liver#imid_993575
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA001767; green = CDH3, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA001767; green = CDH3, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CDH3 IHC & IF
🧪Run placenta first: cytotrophoblasts should stain (HPA: High in placental cytotrophoblasts). Run adipose tissue as the negative comparator, with adipocytes expected to lack detectable staining (HPA: Not detected in adipocytes); on the placenta slide, use areas outside the cytotrophoblast compartment to assess background without assuming those cells are CDH3-negative.
Positive control tissue: Bronchus (Respiratory epithelial cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CDH3 in A-431, CACO-2, U2OS, HaCaT, SK-MEL-30, with annotated localisation: Plasma membrane (supported), Cell Junctions (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; a rabbit IgG isotype control matched to the primary antibody’s clonality; and CDH3 knockout material or a validated peptide-block control (caption: rabbit anti-CDH3 primary; standard IHC practice). Block endogenous peroxidase and check for endogenous biotin in placenta because the documented detection uses a streptavidin–biotin complex with DAB (PA1363 caption: SABC/DAB).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected PA1363 placenta caption does not state a fixative. The documented paraffin-section procedure uses heat retrieval in citrate buffer at pH 6 for 20 minutes (PA1363 caption); frozen-section performance is unreported, while ICC-IF images are available and show plasma membrane and cell-junction localization (HPA subcellular). With the caption’s SABC/DAB method, endogenous biotin can complicate interpretation of placental staining (PA1363 caption; standard IHC practice).
HPA tissue IHC evidence for CDH3
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Nasopharynx | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Oral mucosa | Squamous epithelial cells | High | Protein (IHC) | HPA → |
| Placenta | Cytotrophoblasts | High | Protein (IHC) | HPA → |
| Skin | Cells in basal layer | 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 → |
| Bone marrow | Hematopoietic cells | 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 CDH3 IHC Tips
Troubleshoot CDH3 chromogenic IHC in paraffin sections by checking retrieval, compartment, cell identity and assay controls before scoring.
How should I retrieve CDH3 antigen in paraffin sections?
Start with heat-mediated retrieval in citrate buffer at pH 6 for 20 minutes (datasheet PA1363). The selected placenta-section example used that retrieval before overnight incubation with 1 µg/mL catalog antibody at 4°C (datasheet PA1363). If staining is weak, check heating consistency, section adhesion and positive-control staining before changing retrieval conditions (standard IHC practice). If those checks pass, compare a second retrieval condition on matched sections, keeping antibody concentration and detection constant; judge improvement by junctional staining in expected cells and any accompanying background (UniProt P22223 localization; standard IHC practice).
Could fixation explain weak or patchy CDH3 staining?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative (datasheet PA1363). Record the specimen’s actual fixative, fixation duration and processing history, then compare sections processed alike before attributing differences to CDH3 biology (standard IHC practice). Use the documented citrate pH 6 retrieval for 20 minutes as a starting point and include a positive control in the same run (datasheet PA1363; standard IHC practice). If signal varies with processing history, optimize fixation and retrieval on matched material and assess whether the expected membrane pattern improves without increased diffuse staining (UniProt P22223 localization; standard IHC practice).
What staining pattern supports CDH3 specificity in tissue sections?
Prioritize membrane staining at epithelial cell borders, especially junctions between adjacent cells (UniProt P22223 localization; HPA subcellular: plasma membrane and cell junctions supported). CDH3 has an extracellular region at residues 108–654, a transmembrane segment at 655–677 and a cytoplasmic region at 678–829 (UniProt P22223 topology). In placenta, compare staining with cytotrophoblast morphology; HPA reports high expression in cytotrophoblasts, and the selected product caption shows detection in a placenta section (HPA tissue IHC; datasheet PA1363). Predominantly nuclear or diffuse stromal color warrants review of counterstain, detection background and a no-primary control before interpretation (UniProt P22223 localization; standard IHC practice).
Can this antibody distinguish CDH3 isoforms or epitope accessibility?
The record lists 2 CDH3 isoforms, but the supplied antibody caption does not map its epitope or establish isoform selectivity (UniProt P22223 isoforms; datasheet PA1363). CDH3 processing removes the signal peptide at residues 1–24 and propeptide at 25–107, leaving a reported chain beginning at 108 (UniProt P22223 processing). Its extracellular region includes glycosylation sites at 200 and 566; those annotations alone do not establish that they affect this antibody’s staining (UniProt P22223 topology and glycosylation). Obtain the antibody’s epitope information before assigning staining differences to an isoform, cleavage event or masked epitope (standard IHC interpretation).
How should I assess CDH3 by multiplex IF?
For a parallel IF experiment, pair CDH3 with an epithelial marker such as pan-cytokeratin and inspect cell borders within the expected cell population (HPA tissue IHC: epithelial expression; standard IF practice). HPA supports plasma-membrane and cell-junction localization, so collect separate channels that resolve adjacent cell edges (HPA subcellular; standard IF practice). Select fluorophores after examining an unstained section for tissue autofluorescence, and include single-stain controls to check spectral bleed-through (standard IF practice). Because the supplied caption does not identify the antibody epitope, compare gentle permeabilisation with no permeabilisation: a cytoplasmic-tail epitope requires access to the inner membrane face, while an extracellular epitope may be accessible without it (datasheet PA1363; UniProt P22223 topology; standard IF practice).
How can I reduce diffuse or granular DAB background?
First compare a no-primary control and an expected low-signal region with the stained section; background that persists without primary antibody points toward the detection workflow (standard IHC practice). The selected example uses 10% goat-serum blocking, a biotinylated secondary, streptavidin–biotin detection and DAB (datasheet PA1363). Check peroxidase blocking, secondary-antibody binding and endogenous biotin when using that detection scheme, then adjust one step at a time (standard IHC practice). Keep the 1 µg/mL overnight primary incubation as the documented reference while comparing changes, and accept signal only when expected cell borders remain distinct from diffuse deposit (datasheet PA1363; UniProt P22223 localization; standard IHC practice).
How should I score CDH3 staining across specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring: CDH3 is membrane localized, and HPA reports high staining in placental cytotrophoblasts and several epithelial populations (UniProt P22223 localization; HPA tissue IHC). Record the percentage of cells with convincing membranous staining and intensity on a 0–3 scale; an H-score sums percentage at each intensity and ranges from 0–300 (standard IHC scoring practice). Normalize counts to evaluable target cells, or report positive-cell density per mm² of the same annotated tissue compartment (standard IHC quantification practice). Apply one threshold, exposure-independent brightfield settings and identical exclusion rules for damaged tissue across all slides (standard IHC practice).
When is apparent CDH3 positivity likely to be artefactual?
A credible result places color at cell membranes or junctions in an expected epithelial population; HPA reports high CDH3 in placental cytotrophoblasts and basal skin cells (UniProt P22223 localization; HPA tissue IHC). Treat isolated nuclear staining, broad stromal haze, section-edge accentuation and necrotic deposits as suspect until morphology and controls support them (UniProt P22223 localization; standard IHC interpretation). If color appears in a no-primary control, investigate endogenous peroxidase or detection-system background before calling cells positive (standard IHC practice). Compare the distribution with an expected low-signal population, such as adipocytes, while accounting for tissue quality and the HPA tissue-IHC profile’s medium RNA–staining consistency (HPA tissue IHC).
Boster reagents
Best CDH3 / Cadherin-3 IHC Antibodies
The catalog includes CDH3 antibodies with IHC data from human placenta sections and IF data from human A431 cells (PA1363, A03353-1 and M03353 image captions).
Real IHC data
Anti-P-Cadherin-3 CDH3-Antibody ®
Cat # PA1363
Real IF data
Anti-P-Cadherin-3 CDH3 Antibody ®
Cat # A03353-1
Real IF data
Anti-P-Cadherin-3 CDH3 Antibody ® (monoclonal, 3C9)
Cat # M03353
PA1363 has IHC data from paraffin-embedded human placenta (PA1363 IHC image caption). A03353-1 and M03353 have IF/ICC data from A431 cells (A03353-1 and M03353 IF image captions).
Which to pick: For tissue IHC, choose PA1363: its own caption documents paraffin-embedded human placenta, citrate retrieval at pH 6 for 20 minutes, and DAB detection; the fixative is unreported (PA1363 IHC image caption). For IF/ICC, choose A03353-1 for a rabbit polyclonal antibody or M03353 for mouse monoclonal clone 3C9 (A03353-1 dilution_raw; M03353 catalog entry). No listed SKU has documented cross-species reactivity beyond human (catalog reactivity fields).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P22223 (CADH3_HUMAN, Cadherin-3).
- Human Protein Atlas. CDH3 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. CDH3 subcellular location (ICC-IF): Localized to the plasma membrane and cell junctions..
- Human Protein Atlas. CDH3 antibody validation summary (3 antibodies).
- Alteration of Cadherin 3 Expression and DNA Methylation in Association with Aggressive Renal Cell Carcinoma. International journal of molecular sciences 2023 — PMC10670999.
- mRNA expression of CDH3, IGF2BP3, and BIRC5 in biliary brush cytology specimens is a useful adjunctive tool of cytology for the diagnosis of malignant biliary stricture. Medicine 2016 — PMC5058855.
- Synergistic potential of CDH3 in targeting CRC metastasis and enhancing immunotherapy. BMC cancer 2025 — PMC11951682.
- Secretome proteomics reveals candidate non-invasive biomarkers of BRCA1 deficiency in breast cancer. Oncotarget 2016 — PMC5325383.
- PubMed PMID:2793940 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CDH3 (Cadherin-3). Expected localisation Cell membrane (UniProt). Antigen retrieval: Citrate pH 6 HIER, heat-mediated (datasheet PA1363). Validated IHC antibody: PA1363 at 0.5-1μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Bronchus (Respiratory epithelial cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human placenta tissues; fixative not specified (datasheet PA1363); 2. Fixation: Image fixative and duration unreported (datasheet PA1363); 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: Citrate pH 6 , 20 min (datasheet PA1363); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet PA1363); 8. Primary antibody: Rabbit anti-CDH3, 0.5-1μg/ml (datasheet PA1363); 9. Primary incubation: Overnight at 4 °C (datasheet PA1363). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image PA1363); Caveat: Skin staining may favor basal-layer cells (HPA tissue IHC); Isoform / epitope: 2 isoforms; extracellular vs cytoplasmic epitope matters (UniProt); Regulation: Expression varies across tissues (HPA tissue IHC). Evidence: UniProt P22223, HPA tissue IHC · Enhanced, HPA ICC-IF · plasma membrane and cell junctions., Datasheet PA1363, PMC10670999, PMC5058855. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CDH3/immunohistochemistry-ihc-guide.