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PDK2 / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial · IHC design guide
Design Immunohistochemistry for PDK2
Plan chromogenic PDK2 IHC in paraffin sections using antibody A03261, documented for this application (datasheet A03261). Compare cytoplasmic tissue staining (HPA tissue IHC) with PDK2’s mitochondrial matrix location (UniProt), using the reported cell type variation when interpreting results (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
PDK2 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 | Cytoplasmic tissue staining (HPA tissue IHC); mitochondrial matrix location (UniProt) | |
| Staining pattern | Cytoplasmic staining across tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A03261) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Soft tissue+1 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). Selected-image fixative and duration unreported (datasheet A03261); verify before use. | |
| Caveat | Some fibroblasts show no detectable staining (HPA tissue IHC) | |
| Regulation | Expression varies by tissue (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope differences are unspecified (UniProt) |
Section 1
Recommended PDK2 IHC & IF Protocols
Compare the catalog antibody's IHC-P protocol (datasheet A03261) with a published PDK2 protocol for paraffin-embedded head and neck cancer tissue microarrays (PMC9727917).
| Sample | Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A03261) |
| Fixation | Image fixative and duration unreported (datasheet A03261); 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 A03261); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A03261) |
| Primary antibody | Rabbit anti-PDK2, 2-5μg/ml (datasheet A03261) |
| Primary incubation | Overnight at 4 °C (datasheet A03261) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A03261) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PDK2-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous cytoplasmic expression. No signal in the no-primary control. |
💡Decision noteTry EDTA pH 8.0 heat-mediated retrieval first (datasheet A03261); the published protocol reports antigen retrieval without specifying its buffer or conditions (PMC9727917).
Section 2
What Is the Expected PDK2 Staining Pattern?
PDK2 is a mitochondrial matrix protein with no transmembrane segment (UniProt Q15119: location, topology). In paraffin-section IHC, expect cytoplasmic staining where PDK2 is detected, including adrenal and endometrial glandular cells, bronchial respiratory epithelium, and lymph-node germinal center cells (HPA: tissue IHC). HPA calls its tissue pattern Supported, with medium consistency between antibody staining and RNA expression (HPA: reliability).
| Cytoplasmic staining in adrenal or endometrial glandular cells, bronchial respiratory epithelium, or lymph-node germinal center cells. | These cell types have High staining in HPA tissue IHC (HPA: tissue IHC). Cytoplasmic chromogen fits the reported tissue pattern, although an individual mitochondrial matrix signal may not resolve into visible puncta in a paraffin section (HPA: cytoplasmic expression; UniProt Q15119: mitochondrial matrix). |
| Predominantly nuclear or membranous staining, with little cytoplasmic signal, in an otherwise positive tissue. | Reassess specificity and staining quality: this distribution conflicts with the mitochondrial matrix location and lacks a transmembrane basis (UniProt Q15119: location, topology). Nuclear signal alone is not decisive, because HPA ICC-IF also lists nucleoplasm with uncertain support (HPA: subcellular). |
| Strong staining in soft-tissue fibroblasts or vaginal squamous epithelial cells. | HPA reports PDK2 as Not detected in those respective cell types (HPA: tissue IHC). Check whether the signal follows tissue edges, pigment, or the detection system; cross-reactivity or endogenous activity is possible, but a discrepant cell cannot be classified from one slide alone. |
| Diffuse chromogen across many structures, including spaces or regions without intact cells. | This is difficult to interpret as the reported cellular pattern (HPA: ubiquitous cytoplasmic expression). In chromogenic IHC, inadequate blocking, excess reagent, or incomplete washing can cause nonspecific background (general IHC practice); compare a no-primary control before scoring cells. |
| No staining in a section containing an HPA High cell population. | A blank result in such cells warrants a technical check, but HPA levels describe observed tissue IHC rather than a guarantee for every specimen or antibody (HPA: High tissue IHC; reliability Supported). Review section quality and controls before calling PDK2 absent (general IHC practice). |
💡Expected PDK2 appearanceCall the IHC result compatible when cytoplasmic staining is clear in an HPA High cell population; dominant membrane or nuclear-only chromogen, or staining confined to HPA Not detected cells, calls for review (HPA: tissue IHC; UniProt Q15119: mitochondrial matrix).
| Cell and tissue context | Intensity should be judged within named cell populations: HPA reports High staining in several epithelia and germinal center cells, Low in hepatocytes and adipocytes, and Not detected in soft-tissue fibroblasts (HPA: tissue IHC). These are comparative observations, not universal thresholds. |
| Subcellular location | Matrix localization and the absence of a transmembrane segment support a cytoplasmic IHC interpretation rather than a cell-surface pattern (UniProt Q15119: location, topology). IHC resolution and counterstain can limit recognition of individual mitochondria (general IHC practice). |
| Evidence strength | HPA rates tissue IHC Supported and describes medium agreement with RNA; its listed antibody HPA008287 is IHC Supported (HPA: reliability, antibodies). Treat unexpected staining as a finding to verify, not as proof of a new PDK2 location. |
| Isoforms and antibody epitope | UniProt lists two PDK2 isoforms (UniProt Q15119: isoforms). The supplied sources do not map the catalog antibody epitope, so isoform-specific staining or absence cannot be inferred from this record. |
| IF/ICC Q: What compartment should show signal? | HPA reports supported mitochondrial and uncertain nucleoplasmic localization in ICC-IF (HPA: subcellular). Interpret mitochondrial signal as the stronger location evidence; assess nuclear signal cautiously. IF/ICC methods and controls belong in its separate guide. |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in adrenal glandular cells or bronchial respiratory epithelium. | Both are High in HPA tissue IHC (HPA: tissue IHC); a blank slide may reflect a failed staining step or specimen variation. | Check a concurrently stained positive section, antibody and detection steps, and whether the expected cells are present; adjust routine IHC conditions only after controls identify the failing step (general IHC practice). |
| Nuclei dominate the stain. | This differs from the HPA tissue cytoplasmic profile and UniProt matrix location; ICC-IF nucleoplasm is marked uncertain (HPA: tissue IHC, subcellular; UniProt Q15119: location). | Compare cytoplasm and nuclei in a known-positive cell population and inspect a no-primary control; avoid scoring isolated nuclear chromogen as definitive PDK2 (general IHC practice). |
| Fibroblasts or vaginal squamous cells appear strongly positive. | Those cell types are Not detected in HPA tissue IHC (HPA: tissue IHC); cross-reactivity or detection background is possible. | Check adjacent expected-positive cells and a no-primary control, then repeat with an independently validated antibody if the discrepant pattern persists (general IHC practice). |
| Brown signal spreads beyond cell boundaries. | Diffuse extracellular color does not match the cellular HPA profile (HPA: cytoplasmic expression); nonspecific chromogen deposition is possible (general IHC practice). | Inspect reagent-only controls and review blocking, reagent concentration, washing, and development time before interpreting weak cellular staining (general IHC practice). |
| Blood-rich areas stain despite weak cellular detail. | If peroxidase-based detection was used, endogenous peroxidase can contribute chromogen independently of primary antibody (general IHC practice). | Compare a no-primary control and verify the routine endogenous-peroxidase block for that detection system; score only staining clearly associated with intact cells (general IHC practice). |
| Hepatocytes look faint next to a stronger positive control. | HPA labels hepatocytes Low, so faint cellular staining can fit the reported distribution (HPA: liver hepatocytes Low). | Compare the same cell type across similarly processed sections and use control performance to judge the run; do not require High-cell intensity in hepatocytes (HPA: tissue IHC; general IHC practice). |
Experiment evidence
IHC & IF images showing PDK2 staining
A03261 · IHCIHC analysis of PDK2 using anti-PDK2 antibody (A03261). PDK2 was detected in a paraffin-embedded section of human breast cancer tissue. Heat
A03261 · IHCIHC analysis of PDK2 using anti-PDK2 antibody (A03261). PDK2 was detected in a paraffin-embedded section of human lung cancer tissue. Heat m
A03261 · IFIF analysis of PDK2 using anti-PDK2 antibody (A03261) and anti-Tubulin Alpha antibody (M03989-3). PDK2 was detected in immunocytochemical se
PA1994 · IFIF analysis of PDK2 using anti-PDK2 antibody (PA1994). PDK2 was detected in an immunocytochemical section of A549 cells. Enzyme antigen retr
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000005882-PDK2/tissue/cerebral+cortex#imid_2454216
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000005882-PDK2/tissue/colon#imid_2454158
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000005882-PDK2/tissue/liver#imid_2454151
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000005882-PDK2/tissue/kidney#imid_2454144
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA008287; green = PDK2, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA008287; green = PDK2, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for PDK2 IHC & IF
🧪Run endometrium first: glandular cells should stain for PDK2 (HPA: High in endometrial glandular cells). Use soft tissue fibroblasts as the negative tissue (HPA: Not detected in soft tissue fibroblasts); on the positive slide, adjacent stroma should be assessed for background staining, but its PDK2 status is unreported.
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: Soft tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PDK2 in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (uncertain), Mitochondria (supported) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) slide, a concentration-matched rabbit IgG isotype control for the rabbit catalog antibody, and PDK2-knockout material as a biological negative (selected-SKU caption: rabbit primary; standard IHC control practice). For chromogenic endometrium sections, quench endogenous peroxidase and check any DAB signal in blood-rich areas against the no-primary slide (standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected-SKU paraffin-section caption does not state a fixative (selected-SKU tissue-IHC caption). That caption uses heat-mediated retrieval in EDTA at pH 8.0, but does not establish whether retrieval is required or whether frozen sections are easier (selected-SKU tissue-IHC caption). No matched evidence ranks IF against IHC for ease of use; endometrial blood-rich areas warrant attention when interpreting chromogenic signal (standard IHC practice).
HPA tissue IHC evidence for PDK2
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — 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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in molecular layer | High | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | High | Protein (IHC) | HPA → |
Section 3
Advanced PDK2 IHC Tips
Troubleshoot PDK2 paraffin IHC by checking retrieval, cellular pattern, background controls and scoring against the available tissue evidence (datasheet A03261; HPA tissue IHC).
What retrieval should I try first if PDK2 staining is weak?
Begin with heat-mediated EDTA pH 8.0 retrieval for paraffin PDK2 IHC (datasheet A03261). The selected tissue image used this retrieval before 2 μg/ml primary antibody overnight at 4°C, so reproduce those conditions when diagnosing weak signal (datasheet A03261). Keep heating, cooling and section thickness consistent across comparison slides, since retrieval variation can change staining intensity (standard IHC practice). If staining remains weak, test a modest change in retrieval duration on matched sections while monitoring tissue damage and background (standard IHC practice). Record each condition before comparing cellular staining patterns (standard IHC practice).
Could fixation explain inconsistent PDK2 staining between paraffin sections?
The selected paraffin tissue caption does not state a fixative, so PDK2-specific fixation sensitivity is unknown (datasheet A03261). Record each specimen’s fixative and fixation interval, then compare sections processed together before assigning a staining difference to biology (standard IHC practice). For the reference staining setup, use EDTA pH 8.0 retrieval and 2 μg/ml primary antibody overnight at 4°C to limit other variables (datasheet A03261). If a batch differs, inspect morphology and run matched positive tissue alongside it; uneven preservation or retrieval can mimic variable antigen abundance (standard IHC practice). Do not infer a fixation effect from tissue expression patterns (HPA tissue IHC).
Should PDK2 appear as diffuse cytoplasmic staining or mitochondrial puncta?
PDK2 is assigned to the mitochondrial matrix, with no transmembrane segment (UniProt Q15119). Tissue IHC is described as showing ubiquitous cytoplasmic expression, while subcellular imaging supports mitochondria and labels nucleoplasmic localization uncertain (HPA tissue IHC; HPA subcellular). In chromogenic paraffin sections, assess whether cytoplasmic signal is concentrated in plausible mitochondrial distributions rather than demanding individually resolved puncta (standard IHC practice; UniProt Q15119). Compare the same cell type across sections stained with the 2 μg/ml reference primary concentration and identical DAB development (datasheet A03261; standard IHC practice). Treat predominantly nuclear staining cautiously until an independent control supports it (HPA subcellular; standard IHC practice).
Can this stain distinguish PDK2 isoforms or modified epitopes?
The record lists 2 PDK2 isoforms, but the supplied tissue caption does not map the antibody epitope or establish isoform selectivity (UniProt Q15119; datasheet A03261). PDK2 includes a histidine kinase domain at residues 135–364 and reported modified residues at 215, 216 and 376 (UniProt Q15119). Those annotations alone do not show whether modification or processing changes this antibody’s paraffin staining (UniProt Q15119; standard IHC interpretation). Score the result as PDK2 immunoreactivity, and seek epitope mapping or an orthogonal assay before making isoform-specific claims (standard IHC practice). Keep retrieval and detection conditions matched when comparing specimens (standard IHC practice).
How should I check PDK2 localisation with multiplex immunofluorescence?
Plan at least 2 channels: PDK2 and a validated marker of the cell type being evaluated, such as glandular cells in a tissue where their staining is high (HPA tissue IHC; standard IF practice). Add a mitochondrial marker if channel capacity permits, because mitochondrial localization is supported whereas nucleoplasmic localization is uncertain (HPA subcellular). Select a PDK2 fluorophore in a channel with low measured tissue autofluorescence, and inspect unstained and single-label controls before judging overlap (standard IF practice). Since PDK2 resides in the mitochondrial matrix without a transmembrane segment, optimize post-fixation permeabilisation for access inside mitochondria (UniProt Q15119; standard IF practice). Keep this IF assessment separate from the paraffin IHC protocol (standard assay practice).
How can I reduce diffuse brown background without losing PDK2 signal?
Start from the documented 10% goat serum block, 2 μg/ml primary antibody overnight at 4°C, and DAB detection conditions when troubleshooting the selected paraffin image (datasheet A03261). Include a primary-omission section and a peroxidase-blocking step to assess nonspecific detection and endogenous enzyme activity (standard chromogenic IHC practice). If background persists, compare shorter development or a lower primary concentration on adjacent sections while preserving the same retrieval and washing conditions (standard IHC practice). Examine expected cellular staining separately from pigment, folds and section edges (standard IHC practice). Soft-tissue fibroblasts are reported as undetected, but that observation is a tissue-specific comparison rather than a universal negative control (HPA tissue IHC).
What scoring method makes PDK2 IHC comparable across samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, because tissue IHC reports cytoplasmic staining while mitochondrial localization is supported by subcellular evidence (HPA tissue IHC; HPA subcellular). For comparable regions, report percent positive cells and an H-score using intensity grades 0–3, yielding 0–300 when each grade is weighted by its cell percentage (standard IHC scoring practice). Normalize counts or positive area to the number of eligible cells or evaluable tissue area, and report density per mm² when cell density matters (standard IHC practice). Use identical retrieval, imaging and DAB development settings across batches (standard IHC practice). Record excluded necrotic or damaged regions before analysis (standard IHC practice).
Which PDK2 staining patterns should prompt concern about artefact?
A credible result should fit cytoplasmic tissue staining and the supported mitochondrial location, while predominantly nucleoplasmic localization remains uncertain (HPA tissue IHC; HPA subcellular). Compare cell identities carefully: glandular cells in adrenal gland are reported high, whereas soft-tissue fibroblasts are reported undetected (HPA tissue IHC). Sharp edge-only color, staining restricted to necrotic areas, or signal in the primary-omission section warrants examination for processing, DAB or endogenous-peroxidase artefact (standard IHC practice). Compare suspicious areas with intact neighboring tissue under the same retrieval and detection conditions (standard IHC practice). Do not infer kinase activity from staining intensity alone; the stain measures immunoreactivity (UniProt Q15119; standard IHC interpretation).
Boster reagents
Best PDK2 / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial IHC Antibodies
A03261 has IHC data from human paraffin sections and IF data from human samples (catalog: A03261 image captions); PA1994 has IF/ICC data from A549 cells (catalog: PA1994 image caption).
Real IHC data
Anti-PDK2 Antibody ®
Cat # A03261
Real IF data
Anti-PDK2 Antibody ®
Cat # PA1994
A03261 will render with an IHC figure from a human breast cancer paraffin section; its catalog also lists IHC and IF applications and human, mouse, and rat reactivity (catalog: A03261). PA1994 will render with an IF/ICC figure from A549 cells; its catalog lists IF and ICC applications and human, mouse, and rat reactivity (catalog: PA1994).
Which to pick: Choose A03261 for tissue IHC: its own caption documents a human breast cancer paraffin section, EDTA retrieval at pH 8.0, and primary antibody at 2 μg/ml; the fixative is unreported (catalog: A03261 IHC caption). Choose PA1994 for IF/ICC in cells: its own caption documents A549 cells stained at 5 μg/ml, and its application list includes IF and ICC but excludes IHC (catalog: PA1994 IF caption and applications). For work across species, A03261 lists human, mouse, and rat reactivity and both IHC and IF applications, although its IHC figure shows only a human section; A03261 and PA1994 are rabbit antibodies with no clone specified (catalog: A03261 reactivity, applications, IHC caption, host and clone; PA1994 host and clone).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q15119 (PDK2_HUMAN, [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial).
- Human Protein Atlas. PDK2 tissue IHC expression (reliability: Supported).
- Human Protein Atlas. PDK2 subcellular location (ICC-IF): Mainly localized to the nucleoplasm and mitochondria..
- Human Protein Atlas. PDK2 antibody validation summary (1 antibodies).
- PDK2-enhanced glycolysis aggravates fibrosis via IL11 signaling pathway in Graves' orbitopathy. Frontiers in immunology 2025 — PMC11865214.
- PDK2 leads to cisplatin resistance through suppression of mitochondrial function in ovarian clear cell carcinoma. Cancer science 2021 — PMC8586679.
- PDK1- and PDK2-mediated metabolic reprogramming contributes to the TGFβ1-promoted stem-like properties in head and neck cancer. Cancer & metabolism 2022 — PMC9727917.
- Kidney tissue hypoxia dictates T cell-mediated injury in murine lupus nephritis. Science translational medicine 2020 — PMC8055156.
- PubMed PMID:7499431 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:16625196 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for PDK2 ([Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC); mitochondrial matrix location (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A03261). Validated IHC antibody: A03261 at 2-5μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative Soft tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A03261); 2. Fixation: Image fixative and duration unreported (datasheet A03261); 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 A03261); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A03261); 8. Primary antibody: Rabbit anti-PDK2, 2-5μg/ml (datasheet A03261); 9. Primary incubation: Overnight at 4 °C (datasheet A03261). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific). Selected-image fixative and duration unreported (datasheet A03261); verify before use.; Caveat: Some fibroblasts show no detectable staining (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope differences are unspecified (UniProt); Regulation: Expression varies by tissue (UniProt). Evidence: UniProt Q15119, HPA tissue IHC · Supported, HPA ICC-IF · Mainly localized to the nucleoplasm and mitochondria., Datasheet A03261, PMC9727917. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/PDK2/immunohistochemistry-ihc-guide.