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- Table of Contents
Plan chromogenic PDCD4 IHC around nuclear and cytoplasmic staining in most tissues (HPA tissue IHC). Use breast glandular cells as a high-staining reference (HPA tissue IHC), and score nuclear and cytoplasmic signal separately.
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear and cytoplasmic staining (HPA tissue IHC) | |
| Staining pattern | Nuclear and cytoplasmic signal in most tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A01105) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Lung and colon cancers may show reduced PDCD4 (UniProt) | |
| Regulation | Up-regulated in proliferative cells (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope coverage is unspecified (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet A01105) is paired with three published paraffin-section PDCD4 IHC methods (PMC2976066; PMC6708393; PMC5915117).
| Sample | Paraffin-embedded human appendiceal adenocarcinoma tissue; fixative not specified (datasheet A01105) |
| Fixation | Image fixative and duration unreported (datasheet A01105); 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 A01105); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A01105) |
| Primary antibody | Rabbit anti-PDCD4, 2-5 μg/ml (datasheet A01105) |
| Primary incubation | Overnight at 4 °C (datasheet A01105) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A01105) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PDCD4-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: Nuclear and cytoplasmic expression in most tissues. No signal in the no-primary control. |
PDCD4 staining should be predominantly nuclear, with cytoplasmic staining also possible (UniProt Q53EL6: localisation). HPA reports nuclear and cytoplasmic expression in most tissues, including high staining in breast and colon glandular cells and bone marrow hematopoietic cells (HPA: tissue IHC). Its tissue IHC reliability is Enhanced, with medium consistency between staining and RNA data (HPA: tissue IHC). PDCD4 has no transmembrane segment (UniProt Q53EL6: topology).
| Nuclear staining in glandular cells, with some cytoplasmic signal in the same tissue. | This fits the reported tissue pattern (HPA: nuclear and cytoplasmic expression). Breast and colon glandular cells are useful high-staining examples (HPA: High). Compare signal with neighboring cells and the negative reagent control before judging weak cytoplasmic color (general IHC practice). |
| Staining appears mainly along cell membranes or in acellular material. | A dominant membrane or extracellular pattern does not fit PDCD4’s reported nucleus and cytoplasm localisation or its lack of a transmembrane segment (UniProt Q53EL6: localisation and topology). Check whether the pattern persists without primary antibody; persistent color suggests detection background rather than PDCD4-specific staining (general IHC practice). |
| Strong color is confined to an unexpected cell population while expected cells remain unstained. | Check the cell identity first: high staining is documented in hematopoietic cells, endometrial stromal cells and several epithelial populations (HPA: tissue IHC). If the population is truly unexpected, cross-reactivity or endogenous detection activity is possible (general IHC practice); HPA’s listed low-staining cells are not validated negatives (HPA: Low). |
| Diffuse color covers cells and surrounding tissue without clear nuclear borders. | This pattern cannot establish PDCD4 localisation (general IHC practice). Compare a no-primary control and inspect counterstained morphology; broad background may reflect nonspecific primary binding, incomplete blocking, endogenous enzyme activity or excessive detection development (general IHC practice). The HPA tissue profile supports a cellular nuclear and cytoplasmic pattern (HPA: tissue IHC). |
| No signal is visible in an expected high-staining control section. | First confirm that the control contains the relevant cells: breast or colon glandular cells and bone marrow hematopoietic cells are reported High (HPA: tissue IHC). An absent control signal leaves the sample result uninterpretable; check antibody dilution, retrieval conditions and detection reagents as general IHC troubleshooting, without assuming a PDCD4-specific fixation effect (general IHC practice). |
| Compartment and cell context | PDCD4 shuttles between nucleus and cytoplasm and is predominantly nuclear under normal growth conditions (UniProt Q53EL6: localisation). HPA describes nuclear and cytoplasmic tissue staining, while its ICC-IF summary calls the nucleoplasm the main location (HPA: tissue IHC; HPA: ICC-IF). Score nuclear and cytoplasmic signal separately when both are visible (general IHC practice). |
| Tissue baseline | Appendix, breast, cervix, colon and duodenum glandular cells are reported High; cerebellar granular-layer cells, selected glia and liver cholangiocytes are reported Low (HPA: tissue IHC). A Low designation means reduced expected staining, not a guaranteed blank control (HPA: Low). Match the cell population when comparing sections (general IHC practice). |
| Antibody validation | Two listed antibodies have Enhanced IHC status, while a third has Supported IHC status (HPA: antibody validation). HPA tissue reliability is Enhanced but notes only medium consistency with RNA expression (HPA: tissue IHC). Use these ratings to weigh pattern confidence; they do not establish performance for the catalog antibody or a specific retrieval condition (HPA: antibody validation; general IHC practice). |
| Protein forms and location | UniProt lists two isoforms, no signal peptide or propeptide, one chain spanning residues 1–469, and no transmembrane segment (UniProt Q53EL6: isoforms, processing and topology). Epitope coverage cannot be inferred without the catalog antibody’s immunogen information (general IHC practice). These annotations give no basis for expecting secreted or membrane-restricted PDCD4 staining (UniProt Q53EL6: processing and topology). |
| Retrieval and detection limits | No supplied source establishes PDCD4-specific fixation sensitivity or an optimal retrieval condition (UniProt Q53EL6; HPA: tissue IHC). Retrieval optimization and checks for endogenous detection activity remain general IHC controls (general IHC practice). Interpret any improvement against an expected high-staining control and a no-primary control, rather than treating retrieval response alone as target identity (general IHC practice). |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected high-staining cells are blank in the sample and control. | The run may have lost primary binding or detection signal; HPA reports High staining in breast glandular cells and bone marrow hematopoietic cells (HPA: tissue IHC). | Confirm the control’s cell identity, then check the catalog antibody’s IHC-P instructions, dilution, retrieval setup and detection reagents (general IHC practice). Repeat with a valid positive control before scoring the sample negative (general IHC practice). |
| Nuclei are faint, but diffuse cytoplasmic color is strong. | Some cytoplasmic PDCD4 is plausible, but the expected pattern is predominantly nuclear under normal growth conditions (UniProt Q53EL6: localisation). Diffuse excess color may reflect background (general IHC practice). | Compare with a no-primary control, inspect nuclear borders and titrate primary or detection development if background persists (general IHC practice). Record nuclear and cytoplasmic staining separately (general IHC practice). |
| Membranes, luminal contents or empty spaces stain most strongly. | That dominant pattern conflicts with PDCD4’s nucleus and cytoplasm localisation and absence of a transmembrane segment (UniProt Q53EL6: localisation and topology). | Inspect the no-primary control and morphology, then reassess primary specificity and detection background before calling the section positive (general IHC practice). |
| A low-staining tissue gives weak or variable signal. | HPA lists cerebellar granular-layer cells, selected glia and cholangiocytes as Low, not absent (HPA: tissue IHC). Tissue-wide RNA enrichment in pancreas does not specify staining intensity for every pancreatic cell (HPA: tissue IHC). | Judge the relevant cell type against a documented High control processed in the same run; avoid using a Low tissue as the sole negative control (HPA: tissue IHC; general IHC practice). |
| Brown color persists in the no-primary control. | The color cannot be attributed to primary-antibody binding; endogenous enzyme activity or detection reagents can produce background in chromogenic IHC (general IHC practice). | Check the detection-system controls and the appropriate enzyme-blocking step, then rerun the control alongside the sample (general IHC practice). |
| IF/ICC Q: Where should PDCD4 fluorescence appear? | HPA’s ICC-IF summary identifies the nucleoplasm as the approved main location; its tissue IHC profile also reports cytoplasmic expression (HPA: ICC-IF; HPA: tissue IHC). | A: Expect mainly nucleoplasmic signal in ICC-IF and assess any cytoplasmic signal against appropriate controls; use the separate IF/ICC guide for that application (HPA: ICC-IF; general IF practice). |
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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Cervix | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: PDCD4 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Use the catalog antibody’s paraffin-section example as the starting point, then judge PDCD4 staining by compartment, cell type, and matched controls.
Catalog anti-PDCD4 antibodies have IHC figures for human paraffin sections and mouse brain tissue (A01105 and A01105-1 image captions); no IF figure is supplied (catalog: IF image alts).
A01105 will render with IHC of human appendiceal adenocarcinoma in a paraffin section (A01105 image caption). A01105-1 will render with IHC of mouse brain tissue; its catalog also lists human and rat reactivity, without corresponding IHC figures (A01105-1 image caption; catalog: reactivity).
Which to pick: For human paraffin-section IHC, choose A01105: its own caption reports EDTA retrieval and 2 μg/ml primary antibody, but does not report the fixative (A01105 image caption). For mouse tissue IHC, choose A01105-1; its own mouse brain caption reports 2.5 μg/mL, while the catalog lists human and rat reactivity without IHC figures for those species (A01105-1 image caption; catalog: reactivity). For IF/ICC, M01105 is the listed option, with a monoclonal clone and human/mouse reactivity, but no IF figure is supplied (catalog: M01105 applications, clone, reactivity, IF image alts).