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CDH3 / Cadherin-3 · IHC design guide
Design Immunohistochemistry for CDH3
Plan chromogenic IHC for CDH3 in paraffin sections with the IHC-validated PA1363 antibody (datasheet: PA1363). Use placenta cytotrophoblasts as a positive control and assess membranous staining in squamous epithelia (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 | Membranous in squamous epithelia (HPA tissue IHC) | |
| Staining pattern | Squamous epithelial cells show membranous staining (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 | Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Expression varies by epithelial tissue (HPA tissue IHC) | |
| Isoform / epitope | 2 isoforms; mature extracellular versus cytoplasmic epitope matters (UniProt) |
Section 1
Recommended CDH3 IHC & IF Protocols
The catalog antibody’s citrate pH 6 IHC-P protocol (datasheet PA1363) is paired with a published colon cancer tissue microarray protocol (PMC11951682).
| 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 pH 6 retrieval (datasheet PA1363); the published protocol also uses citrate pH 6, at 80 kPa (PMC11951682).
Section 2
What Is the Expected CDH3 Staining Pattern?
CDH3 is a cell membrane cadherin with an extracellular region, one transmembrane segment and a cytoplasmic tail (UniProt P22223 topology). In paraffin-section IHC, expect epithelial membrane staining, especially in squamous epithelia, basal skin cells, respiratory epithelial cells and placental cytotrophoblasts (HPA tissue IHC). HPA rates its tissue IHC reliability Enhanced, while reporting medium consistency between antibody staining and RNA expression (HPA tissue IHC).
| Distinct staining outlines adjacent epithelial cells, with little signal away from their membranes. | This fits CDH3 at the cell membrane and HPA’s membranous squamous epithelial pattern (UniProt P22223; HPA tissue IHC). Judge the compartment within the relevant cells, rather than treating any dark area as a positive result. |
| Strong nuclear staining or widespread cytoplasmic staining dominates the slide. | Neither is the expected primary location: UniProt assigns CDH3 to the cell membrane, and HPA reports membranous tissue staining (UniProt P22223; HPA tissue IHC). Treat a dominant wrong-compartment pattern as suspect and check detection controls. |
| Strong signal appears in cells expected to be undetected, such as adipocytes in adipose tissue. | HPA reports CDH3 as not detected in adipocytes (HPA tissue IHC). The signal could reflect antibody cross-reactivity or endogenous detection activity; its appearance alone cannot distinguish those causes. |
| Color spreads across tissue and empty spaces, obscuring cell borders. | Diffuse deposition does not establish the reported membranous pattern (HPA tissue IHC). Review blocking, washes and chromogen development as general IHC checks, then compare with a no-primary control. |
| A sampled known-positive region has no visible epithelial membrane signal. | High staining is reported in oral mucosa squamous cells and skin basal-layer cells (HPA tissue IHC). First confirm that the expected cells are present; then check the antibody’s IHC-P instructions and detection controls. Absence alone does not establish CDH3 loss. |
💡Expected CDH3 appearanceCall a result positive when epithelial cell borders show membrane staining, potentially high in oral mucosa squamous cells or skin basal-layer cells (HPA tissue IHC); dominant nuclear color or strong staining in HPA-undetected cells is suspect (UniProt P22223; HPA tissue IHC).
| Which compartment should be scored? | Score epithelial membranes: CDH3 has extracellular residues 108–654, a membrane span at 655–677 and a cytoplasmic tail at 678–829 (UniProt P22223 topology). This record does not identify the antibody epitope. |
| How much should intensity vary by tissue? | HPA reports high staining in bronchus respiratory cells, placenta cytotrophoblasts and tonsil squamous cells, but medium staining in breast glandular cells and cervix squamous cells (HPA tissue IHC). Use the specified cell type when comparing sections. |
| What is a useful negative comparison? | HPA reports no detection in adipocytes, bone-marrow hematopoietic cells and duodenal glandular cells (HPA tissue IHC). These observations are cell-specific; they do not make every cell in those tissues a validated negative control. |
| How strong is the staining evidence? | The tissue profile is rated Enhanced, with medium staining–RNA consistency (HPA tissue IHC). HPA001767 and CAB002487 each have Enhanced IHC status (HPA antibody validation); neither rating proves specificity in a new specimen or workflow. |
| Do processing and isoforms change interpretation? | UniProt lists a signal peptide at 1–24, a propeptide at 25–107, a mature chain at 108–829, two glycosylation sites and two isoforms (UniProt P22223). Their effect on this antibody’s staining is unreported; avoid inferring epitope access or shedding. |
| IF/ICC: what pattern is expected? | HPA supports plasma membrane and cell-junction localisation in ICC-IF (HPA subcellular). That supports the compartment call, but ICC-IF images do not specify an IHC-P retrieval or detection setting. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive epithelium is blank. | The expected cells may be absent from the section, or an IHC workflow step may have failed; HPA reports high staining only in specified cell populations (HPA tissue IHC). | Locate the specified cells first, then review the IHC-validated antibody’s instructions and run appropriate detection controls (general IHC practice). Do not infer target-specific fixation sensitivity from this record. |
| Nuclei dominate the stain. | The pattern conflicts with membrane localisation (UniProt P22223; HPA tissue IHC); the record does not establish which workflow step caused it. | Compare a no-primary control and reassess antibody concentration, washes and detection conditions (general IHC practice). Score membrane signal separately from nuclear color. |
| A nominally negative cell population stains strongly. | For adipocytes or bone-marrow hematopoietic cells, that conflicts with HPA’s not-detected observations (HPA tissue IHC). Cross-reactivity or endogenous detection activity remains possible. | Identify the stained cell type, inspect a no-primary control and check endogenous-activity blocking appropriate to the detection system (general IHC practice). |
| Background obscures cell borders. | Diffuse color prevents assessment of the membranous pattern reported by HPA (HPA tissue IHC); background has several possible workflow causes. | Use a no-primary control, review blocking and washes, and avoid overdeveloping the chromogen (general IHC practice). Reassess only where borders remain interpretable. |
| A weak breast glandular-cell signal seems inconsistent with a stronger oral mucosa control. | HPA reports medium staining in breast glandular cells and high staining in oral mucosa squamous cells (HPA tissue IHC). Equal intensity is not the expected benchmark. | Compare the correct cells and their membrane pattern before calling a weak result abnormal; retain the tissue-specific HPA levels as context (HPA tissue IHC). |
| Staining is present but its location is hard to judge. | Crowded or overlapping cells can obscure borders in an IHC section (general IHC practice); color alone cannot confirm membrane localisation. | Inspect a well-preserved area at higher magnification and use the counterstain to identify cells (general IHC practice). Call CDH3 positive only when the relevant epithelial membranes are interpretable (UniProt P22223; HPA tissue IHC). |
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 cytotrophoblasts; PA1363 IHC caption: placenta). Use adipose tissue as the negative tissue: adipocytes should lack detectable staining (HPA: Not detected in adipocytes); on the placenta slide, cells without junctional signal should appear at background level, but the supplied evidence does not identify a specific negative placental cell type (HPA subcellular: plasma membrane and cell junctions).
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) slide, a concentration-matched rabbit immunoglobulin isotype control, and a CDH3-knockout biological negative (PA1363 IHC caption: rabbit primary; standard IHC practice). For placenta, check endogenous peroxidase and biotin background because the documented detection uses biotin and DAB (PA1363 IHC caption: biotinylated secondary, streptavidin–biotin complex, DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected PA1363 paraffin-section caption does not state the fixative (PA1363 IHC caption: fixative unreported). The documented IHC used citrate retrieval at pH 6 for 20 minutes; whether staining depends on retrieval is unreported (PA1363 IHC caption). ICC-IF images support membrane and junctional localisation, but the supplied evidence does not establish that IF or frozen sections are easier than paraffin IHC; placental endogenous biotin may complicate the documented biotin-based detection (HPA subcellular: plasma membrane and cell junctions; PA1363 IHC caption: biotin-based detection; 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 staining in paraffin sections by checking retrieval, membrane localisation, cell identity and controls before interpreting chromogenic signal.
How should I retrieve CDH3 when junctional staining is weak in paraffin sections?
Start with heat-mediated citrate retrieval at pH 6 for 20 minutes on paraffin sections (datasheet PA1363). The catalog antibody produced CDH3 staining in a human placenta section under those conditions, although the caption does not report its fixative (datasheet PA1363). If junctional signal is weak, compare retrieval conditions on adjacent sections while holding antibody concentration, detection and development constant (standard IHC practice). Judge improvement by cleaner cell-border staining in expected positive cells, including placental cytotrophoblasts, rather than by a general increase in brown signal (HPA: High in placental cytotrophoblasts; HPA: membranous expression). Keep a no-primary control alongside each comparison to expose retrieval-related background (standard IHC practice).
Could fixation explain weak or uneven CDH3 staining?
Target-specific sensitivity of CDH3 staining to fixation is unknown from the supplied evidence; the catalog antibody’s paraffin-section caption does not state a fixative (datasheet PA1363). Record the fixative, fixation duration and processing history for each specimen before comparing staining intensity (standard IHC practice). When troubleshooting variable sections, stain a consistently processed positive control alongside them and keep citrate retrieval at pH 6 for 20 minutes constant (datasheet PA1363; standard IHC practice). Compare intact epithelial borders within similarly preserved areas, since tissue damage and uneven processing can complicate chromogenic scoring (standard IHC practice). Do not assign a CDH3-specific fixation effect from localisation or tissue-expression data alone (UniProt P22223 topology; HPA: tissue IHC profile).
Where should convincing CDH3 chromogenic signal appear?
Expect CDH3 mainly at cell borders: UniProt places it at the cell membrane, and HPA supports plasma-membrane and cell-junction localisation (UniProt P22223 subcellular location; HPA: subcellular). Its extracellular region spans residues 108–654, followed by a transmembrane segment at 655–677 and a cytoplasmic region at 678–829 (UniProt P22223 topology). In sections, look for coherent membranous staining in the appropriate epithelial population rather than diffuse colour across every compartment (HPA: membranous expression in squamous epithelia; standard IHC practice). Placental cytotrophoblasts provide one documented high-expression comparator for the catalog antibody’s placenta image (HPA: High in placental cytotrophoblasts; datasheet PA1363). Treat predominantly nuclear staining as a prompt to check controls and morphology before assigning CDH3 positivity (UniProt P22223 subcellular location; standard IHC practice).
How can epitope location affect interpretation of CDH3 staining?
CDH3 has 2 recorded isoforms, but the supplied evidence does not map the catalog antibody’s epitope or establish its isoform coverage (UniProt P22223 isoforms; datasheet PA1363). The mature chain begins at residue 108; residues 108–654 are extracellular and 678–829 are cytoplasmic (UniProt P22223 processing and topology). Glycosylation is recorded at residues 200 and 566, both within the extracellular region, without evidence here that either site changes this antibody’s tissue staining (UniProt P22223 glycosylation and topology). Obtain epitope-mapping evidence before treating loss of staining as isoform loss or glycan masking (standard IHC interpretation). Meanwhile, compare like-processed sections using the same citrate pH 6 retrieval and membrane-focused scoring (datasheet PA1363; HPA: membranous expression).
How can IF help assess an ambiguous chromogenic CDH3 pattern?
Use IF as a separate localisation check when chromogenic IHC leaves cell borders or cell identity uncertain (standard IHC/IF practice). Multiplex CDH3 with a validated marker for the expected cell population, such as a cytotrophoblast identity marker when examining placenta, and assess whether their cell assignments agree (HPA: High in placental cytotrophoblasts; standard IF practice). Choose spectrally separated fluorophores and favour a longer-wavelength channel when tissue autofluorescence interferes with CDH3 detection (standard IF practice). If the antibody recognises an extracellular epitope, limit permeabilisation; if it recognises the cytoplasmic region, optimise permeabilisation to permit access (UniProt P22223 topology; standard IF practice). The supplied catalog evidence documents paraffin-section IHC, not IF performance or the antibody’s epitope side (datasheet PA1363).
How do I distinguish CDH3 staining from chromogenic background?
Run a no-primary section and inspect blank areas, damaged edges and non-target cells before increasing antibody or chromogen exposure (standard IHC practice). The catalog example used 1 µg/ml primary antibody, 10% goat-serum block, a biotinylated secondary, streptavidin–biotin detection and DAB (datasheet PA1363). With that detection chemistry, evaluate endogenous biotin and nonspecific secondary binding if widespread brown signal persists in controls (standard IHC practice). Include a peroxidase block when using DAB as a general chromogenic workflow step, then compare development across matched sections (standard IHC practice). Credible CDH3 signal should favour epithelial cell borders over uniform staining of unrelated structures (HPA: membranous expression in squamous epithelia; UniProt P22223 subcellular location).
How should I quantify CDH3 across specimens with different epithelial content? ⚠ ANSWER MARKED FOR VERIFICATION
Define the region and cell population before scoring, and exclude damaged or necrotic areas using the accompanying morphology (standard IHC practice). Record the percentage of viable target cells with membranous staining and, when intensity matters, score those cells from 0–3 to calculate an H-score from 0–300 (standard IHC scoring practice; HPA: membranous expression). Normalise positive-cell counts to the total viable cells in the same annotated population, rather than to all cells in a section containing different amounts of epithelium (standard IHC practice). Apply identical retrieval, imaging and DAB development across specimens before comparing scores (datasheet PA1363; standard IHC practice). Report cytoplasmic-only signal separately because the supported reference pattern is membranous and junctional (HPA: subcellular).
What evidence makes an apparent CDH3-positive section convincing?
A convincing result shows cell-border staining in an expected population, with appropriate morphology and little signal in the no-primary control (HPA: membranous expression; UniProt P22223 subcellular location; standard IHC practice). Placental cytotrophoblasts and squamous epithelial cells in oral mucosa are documented high-expression comparators, whereas adipocytes are listed as not detected (HPA: tissue IHC). Check whether colour instead concentrates at section edges, necrotic regions or sites of endogenous enzyme activity before calling the tissue positive (standard IHC practice). Predominantly nuclear staining is discordant with the supported membrane and junction localisation and needs independent validation (HPA: subcellular; standard IHC interpretation). Interpret weak cases cautiously because HPA rates tissue staining as Enhanced but describes only medium consistency with RNA expression (HPA: tissue IHC reliability).
Boster reagents
Best CDH3 / Cadherin-3 IHC Antibodies
Human-reactive CDH3 antibodies have real paraffin-section IHC data from placenta and IF/ICC data from A431 cells (PA1363 IHC caption; A03353-1 and M03353 IF 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 is listed for human IHC and was shown on a paraffin-embedded human placenta section (PA1363 applications and IHC caption). A03353-1 and M03353 are listed for human IF/ICC, with A431 cell images for each (A03353-1 and M03353 applications and IF captions).
Which to pick: Choose PA1363 for chromogenic IHC on paraffin sections: its placenta caption describes citrate retrieval at pH 6 for 20 minutes and DAB detection; the fixative is unreported (PA1363 IHC caption). For IF/ICC, choose A03353-1 if a rabbit antibody suits the detection setup, or M03353 for mouse monoclonal clone 3C9; both have A431 IF images (A03353-1 and M03353 catalog entries and IF captions). None of these SKUs has documented reactivity beyond human, so this payload does not support a cross-species choice (catalog reactivity).
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 Membranous in squamous epithelia (HPA tissue IHC). 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: Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific); Caveat: Staining and RNA show medium consistency (HPA tissue IHC); Isoform / epitope: 2 isoforms; mature extracellular versus cytoplasmic epitope matters (UniProt); Regulation: Expression varies by epithelial tissue (HPA tissue IHC). Evidence: UniProt P22223, HPA tissue IHC · Enhanced, HPA ICC-IF · plasma membrane and cell junctions., Datasheet PA1363, PMC11951682. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CDH3/immunohistochemistry-ihc-guide.