PDCD4 / Programmed cell death protein 4 · IHC design guide

Design Immunohistochemistry for PDCD4

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.

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for PDCD4 (IHC for PDCD4): expected localisation Nuclear and cytoplasmic staining (HPA tissue IHC), antibody A01105, validated IHC image, and IHC protocol steps
Printable PDCD4 IHC protocol sheet — expected localisation Nuclear and cytoplasmic staining (HPA tissue IHC), antibody A01105, controls and protocol steps. Open the full PDCD4 IHC guide →

PDCD4 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 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
Important caveats
Reasons your staining may differ from the expected pattern.
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)
Section 1

Recommended PDCD4 IHC & IF Protocols

The catalog antibody’s IHC-P protocol (datasheet A01105) is paired with three published paraffin-section PDCD4 IHC methods (PMC2976066; PMC6708393; PMC5915117).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human appendiceal adenocarcinoma tissue; fixative not specified (datasheet A01105)
FixationImage fixative and duration unreported (datasheet A01105); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet A01105); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A01105)
Primary antibodyRabbit anti-PDCD4, 2-5 μg/ml (datasheet A01105)
Primary incubationOvernight at 4 °C (datasheet A01105)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet A01105)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultPDCD4-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.
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A01105); use citrate pH 6 when reproducing the pleural study (PMC5915117).
Section 2

What Is the Expected PDCD4 Staining Pattern?

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).

What am I looking at on my slide?
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).
💡Expected PDCD4 appearanceA convincing positive shows discernible, predominantly nuclear staining, with possible cytoplasmic staining, in a documented high-staining cell population such as breast glandular cells (UniProt Q53EL6: localisation; HPA: High); isolated membrane or acellular color is suspect (UniProt Q53EL6: topology; general IHC practice).
How each factor affects the staining
Compartment and cell contextPDCD4 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 baselineAppendix, 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 validationTwo 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 locationUniProt 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 limitsNo 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).
Why is my staining missing, weak or wrong?
SituationLikely causeNext 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).

Sample controls for PDCD4 IHC & IF

🧪Run appendix first and assess glandular cells, which show high PDCD4 staining (HPA: High in appendix glandular cells). HPA detects PDCD4 in all 45 scored tissues, so no negative tissue is available; use no-primary and isotype controls, and expect cells without specific staining on the positive slide to show counterstain alone without treating them as proven PDCD4-negative (HPA: no negative rows; standard IHC control interpretation).
Positive control tissue: Appendix (Glandular cells, HPA High)
Negative control tissue: None in HPA: PDCD4 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PDCD4 in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide, a rabbit IgG isotype control matched to the primary antibody’s clonality and concentration, and a PDCD4 knockout specimen as a biological negative (caption: rabbit primary; standard IHC practice). Block endogenous peroxidase in appendix sections before HRP/DAB detection and assess background in the controls (caption: appendix section with HRP/DAB detection; standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected A01105 paraffin-section caption does not state a fixative (caption: fixative unreported). The caption reports heat-mediated retrieval in EDTA at pH 8.0, but does not establish whether retrieval is required or whether frozen sections or IF are easier (caption: EDTA retrieval; evidence unreported for alternatives). Endogenous peroxidase can confound HRP/DAB staining in the appendix and should be checked with the negative controls (caption: appendix section with HRP/DAB detection; standard IHC practice).

HPA tissue IHC evidence for PDCD4

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

TissueCell typeLevelEvidenceSource
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 →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
None in HPA: PDCD4 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced PDCD4 IHC Tips

Use the catalog antibody’s paraffin-section example as the starting point, then judge PDCD4 staining by compartment, cell type, and matched controls.

How should I retrieve PDCD4 in paraffin sections when nuclear staining is weak?
Start with heat-mediated antigen retrieval in EDTA at pH 8.0 (datasheet A01105). The selected paraffin-section example used that retrieval before 10% goat-serum blocking and 2 μg/ml primary antibody overnight at 4°C (datasheet A01105). If staining remains weak, adjust heating duration on matched sections while holding antibody concentration and detection conditions constant; assess tissue preservation alongside signal (standard IHC practice). Compare nuclear and cytoplasmic staining in appendix glandular cells, which show high PDCD4 staining, and include a no-primary control to distinguish failed retrieval from detection background (HPA: High in appendix glandular cells; standard IHC practice).
Could fixation explain inconsistent PDCD4 staining across my paraffin blocks?
Target-specific PDCD4 fixation sensitivity is unknown from the supplied evidence; the selected example identifies a paraffin section but does not state its fixative (datasheet A01105). Record each block’s fixative and processing history before comparing staining, because variable fixation and processing can change antigen accessibility in routine IHC (standard IHC practice). Run suspect and well-performing sections together with the same EDTA pH 8.0 retrieval and 2 μg/ml primary-antibody condition used in the example (datasheet A01105). If the difference persists, inspect morphology and matched controls before assigning it to fixation; neither tissue expression patterns nor protein topology establishes a PDCD4-specific fixation effect (standard IHC practice).
Should I reject cytoplasmic PDCD4 staining when nuclei also stain?
Assess nuclear and cytoplasmic compartments separately: PDCD4 is reported in both and can shuttle between them (UniProt Q53EL6: subcellular localisation). Predominantly nuclear localisation under normal growth conditions supports a nuclear reference pattern, while HPA reports nuclear and cytoplasmic staining in most tissues (UniProt Q53EL6: subcellular localisation; HPA: tissue IHC profile). Score staining within identifiable cells rather than treating diffuse chromogen outside cell boundaries as cytoplasmic signal (standard IHC practice). If a compartment changes between sections, check retrieval, counterstain, and tissue integrity first, then compare matched cellular regions; a localisation shift alone does not establish a change in PDCD4 activity (standard IHC practice).
How can I troubleshoot staining differences if the antibody epitope is unspecified?
PDCD4 has 2 reported isoforms, but the supplied catalog example does not identify the antibody’s epitope or isoform coverage (UniProt Q53EL6: isoforms; datasheet A01105). The protein has MI domains at residues 163–284 and 326–449, plus reported phosphorylation sites including Ser-67; those facts do not locate this antibody’s binding site (UniProt Q53EL6: domains and modified residues). Ask for an epitope map or isoform reactivity data before interpreting a staining difference as isoform-specific (standard IHC practice). Meanwhile, compare matched sections under identical retrieval and detection conditions, using a no-primary control and a documented positive tissue region to separate background or processing variation from a reproducible pattern (standard IHC practice; HPA: High in appendix glandular cells).
How should I adapt this PDCD4 IHC evidence for a multiplex IF experiment?
Treat IF as a separate assay: the selected A01105 example documents chromogenic staining of a paraffin section, while HPA reports PDCD4 mainly in the nucleoplasm in its subcellular images (datasheet A01105; HPA: subcellular localisation). Multiplex with a marker for the cell population under study, and inspect whether PDCD4 signal falls within those cells’ nuclei or cytoplasm (standard IF practice; UniProt Q53EL6: subcellular localisation). Choose a fluorophore channel after checking unstained tissue autofluorescence and single-stain controls, then set exposure without saturating the PDCD4 channel (standard IF practice). Because PDCD4 has no transmembrane segment and is intracellular, establish permeabilisation for the nuclear or cytoplasmic epitope being assessed; IF fixation and antibody-specific IF performance remain unreported here (UniProt Q53EL6: topology and localisation; datasheet A01105).
What should I check when DAB obscures PDCD4 cell boundaries?
The selected paraffin-section example used a peroxidase-conjugated secondary antibody and DAB, so inspect both primary-dependent staining and detection-system background (datasheet A01105). Include a no-primary section and apply a peroxidase block as a routine chromogenic IHC control; review whether pigment or precipitate persists without primary antibody (standard IHC practice). Keep the example’s 10% goat-serum block and 2 μg/ml primary condition as a reference while changing one variable at a time (datasheet A01105; standard IHC practice). If signal pools at cut edges or damaged areas, score intact tissue away from those regions and compare nuclear detail before calling diffuse brown material PDCD4-positive (standard IHC practice).
How should I quantify nuclear and cytoplasmic PDCD4 across sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and tissue area before scoring, then report nuclear and cytoplasmic PDCD4 separately because both compartments are documented (standard IHC practice; HPA: tissue IHC profile). For a cell-based readout, record the percentage of positive cells and an H-score from staining intensity and positive-cell fractions, using the same thresholds across sections (standard IHC practice). Normalise counts or positive-cell density to evaluable tissue area in mm², and exclude folds, necrosis, and section edges according to a prespecified rule (standard IHC practice). Record retrieval and detection settings alongside scores; HPA describes only medium consistency between staining and RNA expression, so RNA abundance alone should not set the staining threshold (HPA: Enhanced reliability description).
How can I distinguish genuine PDCD4 staining from section artefacts?
Look for cell-contained nuclear or cytoplasmic signal: both are reported for PDCD4, and appendix glandular cells provide a documented high-staining reference (UniProt Q53EL6: subcellular localisation; HPA: tissue IHC profile and High in appendix glandular cells). Treat staining confined to cut edges, necrotic regions, or areas without intact cells as suspect, and compare those regions with preserved tissue on the same section (standard IHC practice). Check a no-primary control and the peroxidase block when brown deposits appear broadly, because the selected example uses peroxidase detection with DAB (standard IHC practice; datasheet A01105). Finally, record which cell type and compartment stained; reduced PDCD4 expression reported in lung cancer and colon carcinoma does not make every unstained cell an assay failure (UniProt Q53EL6: tissue specificity).
Boster reagents

Best PDCD4 / Programmed cell death protein 4 IHC Antibodies

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).

Real IHC data IHC analysis of PDCD4 using anti-PDCD4 antibody (A01105). PDCD4 was detected in a paraffin-embedded section of human appendiceal adenocarcinoma tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-PDCD4 Antibody (A01105) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-PDCD4 Antibody ®
Cat # A01105
Real IHC data Immunohistochemistry of PDCD4 in mouse brain tissue with PDCD antibody at 2.5 μg/mL.
Anti-PDCD4 Antibody
Cat # A01105-1

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).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q53EL6 (PDCD4_HUMAN, Programmed cell death protein 4).
  2. Human Protein Atlas. PDCD4 tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. PDCD4 subcellular location (ICC-IF): Mainly localized to the nucleoplasm..
  4. Human Protein Atlas. PDCD4 antibody validation summary (3 antibodies).
  5. Programmed cell death 4 (PDCD4) expression during multistep Barrett's carcinogenesis. Journal of clinical pathology 2010 — PMC2976066.
  6. Programmed cell death 4 (PDCD4) as a novel prognostic marker for papillary thyroid carcinoma. Cancer management and research 2019 — PMC6708393.
  7. MicroRNA expression in lung tissues of asbestos-exposed mice: Upregulation of miR-21 and downregulation of tumor suppressor genes Pdcd4 and Reck. Journal of occupational health 2021 — PMC8535435.
  8. MiR-21 over-expression and Programmed Cell Death 4 down-regulation features malignant pleural mesothelioma. Oncotarget 2018 — PMC5915117.
  9. PubMed PMID:9759869 — UniProt-cited evidence.
  10. PubMed PMID:14702039 — UniProt-cited evidence.
  11. PubMed PMID:15164054 — UniProt-cited evidence.