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PDK2 / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial · IHC design guide
Design Immunohistochemistry for PDK2
Plan PDK2 staining in paraffin sections using its observed cytoplasmic tissue pattern (HPA tissue IHC) and expected mitochondrial matrix location (UniProt). The guide covers fixation consistency, chromogenic detection and interpretation of variable staining intensity (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 | Observed cytoplasmic staining; mitochondrial matrix expected (HPA tissue IHC; UniProt) | |
| Staining pattern | Widespread cytoplasmic staining with variable intensity (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 conditions consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Staining and RNA expression show medium consistency (HPA tissue IHC) | |
| Regulation | Expression varies by tissue (UniProt) | |
| Isoform / epitope | Two isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended PDK2 IHC & IF Protocols
The catalog antibody protocol (datasheet A03261) is accompanied by one published IHC protocol using 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 noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A03261); the published protocol reports antigen retrieval without specifying its conditions (PMC9727917).
Section 2
What Is the Expected PDK2 Staining Pattern?
Expect PDK2 staining mainly in the cytoplasm, consistent with its mitochondrial matrix location and lack of a transmembrane segment (UniProt Q15119). HPA describes ubiquitous cytoplasmic tissue staining, with high staining in selected glandular, epithelial, hematopoietic and germinal center cells (HPA tissue IHC). Tissue IHC reliability is Supported, with medium agreement between antibody staining and RNA expression (HPA tissue IHC).
| Cytoplasmic, granular staining in adrenal glandular cells, bronchial respiratory epithelial cells or bone marrow hematopoietic cells. | This fits the expected mitochondrial compartment (UniProt Q15119) and cell types scored High by HPA tissue IHC. Granularity is a plausible appearance for mitochondrial staining, but chromogenic IHC alone does not establish that every stained structure is a mitochondrion (general IHC practice). |
| Predominantly nuclear staining, with little or no cytoplasmic signal. | Recheck specificity and detection: the established location is mitochondrial (UniProt Q15119; HPA subcellular: supported), while HPA calls its IF nucleoplasmic assignment uncertain. Nuclear staining alone is therefore insufficient to call a correct PDK2 IHC pattern; it may reflect artefact or nonspecific staining. |
| Strong staining in soft tissue fibroblasts or vaginal squamous epithelial cells. | HPA reports PDK2 as Not detected in those cells (HPA tissue IHC). Consider cross-reactivity or endogenous detection activity, especially if staining persists in a no-primary control (general IHC practice). Check that tissue identity and the stained cell type match the reference before assigning a false positive. |
| Diffuse color across cells and extracellular areas, obscuring cytoplasmic detail. | This cannot be scored confidently against HPA’s cytoplasmic pattern (HPA tissue IHC). Excess detection reagent, incomplete blocking or inadequate washing can create background (general IHC practice). Assess a no-primary control and reduce background before interpreting the apparent tissue distribution. |
| No convincing signal in adrenal glandular cells or bone marrow hematopoietic cells. | Both are High reference cell populations (HPA tissue IHC), so their absence warrants a technical check. Verify that the cells are present and examine antibody dilution, antigen retrieval and detection controls (general IHC practice). The supplied sources do not establish a PDK2-specific fixation or retrieval failure. |
💡Expected PDK2 appearanceCall a positive result when identifiable HPA High cell populations show clear cytoplasmic staining compatible with mitochondrial PDK2 (HPA tissue IHC; UniProt Q15119); isolated nuclear color or strong staining in HPA Not detected cells needs further specificity checks (HPA subcellular: nuclear uncertain; HPA tissue IHC).
| Compartment | PDK2 is a mitochondrial matrix protein without a transmembrane segment (UniProt Q15119). Interpret tissue IHC against the HPA cytoplasmic pattern; HPA’s IF mitochondrial assignment is supported, while its nucleoplasmic assignment is uncertain (HPA tissue IHC; HPA subcellular). |
| Cell and tissue selection | HPA scores adrenal glandular cells and bronchial respiratory epithelial cells High, liver hepatocytes Low, and soft tissue fibroblasts Not detected (HPA tissue IHC). Compare matched cell populations within tissue; a whole-section impression can conceal these differences (general IHC practice). |
| Strength of reference evidence | HPA labels tissue IHC reliability Supported and describes medium agreement with RNA expression; the listed antibody HPA008287 is IHC Supported (HPA tissue IHC; HPA antibodies). Treat the reported distribution as a useful reference, with room for antibody and sample-level variation. |
| Isoforms and epitope coverage | UniProt lists two PDK2 isoforms (UniProt Q15119). Without an epitope map or isoform-specific validation in the supplied evidence, staining cannot identify which isoform contributes to a cell’s signal; review antibody documentation if isoform discrimination matters (general IHC practice). |
| Antigen retrieval | Retrieval is a standard paraffin-IHC workflow variable (general IHC practice). The supplied UniProt and HPA records provide no PDK2-specific retrieval condition or fixation-sensitivity claim, so optimize using assay controls rather than predicting an effect for a particular tissue. |
| Detection background | Endogenous enzyme activity and nonspecific reagent binding can produce chromogenic color independently of primary-antibody binding (general IHC practice). No-primary and detection controls help distinguish that background from the cytoplasmic cell pattern reported by HPA (HPA tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| High reference cells have no staining. | Possible failed antibody or detection step, overly dilute reagent, or unsuitable retrieval (general IHC practice); no PDK2-specific fixation effect is established here. | Confirm the expected cells are present, run a positive tissue control, and check antibody dilution, retrieval and detection in sequence (general IHC practice; HPA tissue IHC: adrenal glandular cells High). |
| Only nuclei stain strongly. | A nuclear-only result does not match supported mitochondrial localization (UniProt Q15119; HPA subcellular). HPA’s nucleoplasmic IF assignment is uncertain (HPA subcellular). | Review morphology and a no-primary control, then reassess antibody specificity before scoring nuclei as PDK2 positive (general IHC practice; HPA subcellular). |
| Soft tissue fibroblasts show strong color. | That cell type is Not detected in the HPA tissue reference (HPA tissue IHC); cross-reactivity or endogenous detection activity is possible (general IHC practice). | Confirm the cell identity, inspect no-primary staining, and compare with an HPA High cell population processed in the same run (HPA tissue IHC; general IHC practice). |
| Color is diffuse across the section. | Background from incomplete blocking, excess reagent or insufficient washing may obscure the reported cytoplasmic pattern (general IHC practice; HPA tissue IHC). | Check no-primary and detection controls, then adjust blocking, reagent concentration and washes before scoring cellular intensity (general IHC practice). |
| Low reference cells look as dark as High reference cells. | Overdeveloped chromogen or saturated detection can compress apparent intensity differences (general IHC practice); HPA scores liver hepatocytes Low and adrenal glandular cells High (HPA tissue IHC). | Compare identifiable cell types under the same processing and shorten chromogen development or adjust detection if signal is saturated (general IHC practice; HPA tissue IHC). |
| IF shows mitochondria plus apparent nuclear signal. | HPA supports the mitochondrial IF location but marks nucleoplasmic localization uncertain (HPA subcellular). | Keep IF interpretation on its separate guide page; for this IHC assessment, prioritize the supported mitochondrial and tissue-cytoplasmic pattern and validate nuclear signal independently (HPA subcellular; HPA tissue IHC). |
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 (HPA: High in endometrial glandular cells). Use vaginal squamous epithelium as a negative tissue (HPA: Not detected); on the positive slide, independently verified negative cells should lack specific DAB staining, since HPA does not identify an internal negative cell population in endometrium.
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 no-primary (secondary-only), a rabbit IgG isotype control matched to the primary antibody where appropriate, and PDK2 knockout tissue or a validated peptide-block control (selected-SKU caption: rabbit primary antibody). Block endogenous peroxidase and inspect blood-containing areas for background before interpreting DAB staining (selected-SKU caption: peroxidase detection with DAB).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the fixative is unreported in the selected-SKU paraffin-section caption. Heat retrieval in EDTA at pH 8.0 is a documented starting condition; a requirement for that retrieval method has not been established (selected-SKU caption: EDTA retrieval). The supplied evidence does not establish that frozen sections or IF are easier; for IF, mitochondrial localization is supported while nucleoplasmic localization is uncertain (HPA subcellular).
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 chromogenic IHC by checking retrieval, staining controls, and whether the signal fits its mitochondrial localisation (UniProt Q15119; HPA subcellular).
How should I retrieve PDK2 in paraffin sections when staining is weak?
Start with heat-mediated antigen retrieval in EDTA at pH 8.0 (datasheet A03261). The selected paraffin-section image used this condition before overnight incubation with 2 μg/ml antibody at 4°C (caption A03261). If staining remains weak, compare a second retrieval condition on serial sections while holding antibody concentration, detection, and exposure to DAB constant (standard IHC practice). Include a positive control with glandular cells from adrenal gland and a no-primary control; the former has high reported staining, while the latter helps identify detection-related colour (HPA: High in adrenal gland glandular cells; standard IHC practice).
Could fixation explain weak or uneven PDK2 staining?
Target-specific sensitivity of PDK2 staining to fixation is unknown: the selected paraffin-section caption does not state a fixative (caption A03261). Record fixative, fixation duration, section age, and processing history for each specimen before comparing staining intensity (standard IHC practice). For weak or uneven staining, compare sections processed together and apply the same EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody conditions used in the selected image (datasheet A03261; caption A03261). Use a positive control in the same run to separate a batch-wide staining failure from specimen-level variation, without assigning either outcome to a PDK2-specific fixation effect (standard IHC practice).
Where should convincing PDK2 chromogenic signal appear?
Evaluate staining principally within cell cytoplasm, looking for a punctate pattern compatible with mitochondria: PDK2 is assigned to the mitochondrial matrix, and HPA supports a mitochondrial location (UniProt Q15119 subcellular; HPA subcellular). HPA also describes ubiquitous cytoplasmic tissue staining, so a broader cytoplasmic appearance in chromogenic sections needs comparison with controls rather than automatic rejection (HPA tissue IHC; standard IHC practice). Treat isolated nuclear staining cautiously because HPA marks its nucleoplasmic assignment uncertain (HPA subcellular). Compare the same cell type across serial sections and inspect morphology and no-primary controls before calling a faint cytoplasmic deposit specific (standard IHC practice).
Can this stain distinguish PDK2 isoforms or modification states?
Do not score isoforms 1 and 2 separately from this stain without an isoform-specific epitope and validation; the record lists both isoforms, but the selected caption supplies no epitope map (UniProt Q15119 isoforms; caption A03261). PDK2 has a histidine kinase domain at residues 135–364 and reported modifications at Tyr 215, Tyr 216, and Lys 376 (UniProt Q15119 domains and modified residues). Those annotations alone do not establish whether modification or processing changes antibody binding in a section (standard IHC interpretation). Check the antibody's epitope documentation and compare a second validated reagent if isoform or modification specificity is essential (standard IHC practice).
How would I check the IHC pattern by multiplex IF?
Use IF as a separate localisation check and establish its staining conditions independently of the paraffin-section IHC caption (caption A03261; standard IF practice). Pair PDK2 with a validated mitochondrial marker and, where cell identity matters, a marker for the expected cell population; mitochondrial localisation is supported, while nucleoplasmic localisation remains uncertain (HPA subcellular). Choose fluorophores away from the specimen's strongest autofluorescence and inspect single-stain and no-primary controls before interpreting overlap (standard IF practice). Because PDK2 is assigned to the mitochondrial matrix and has no transmembrane segment, optimise permeabilisation for access inside mitochondria while monitoring organelle morphology and marker retention (UniProt Q15119 subcellular and topology; standard IF practice).
What should I check when DAB background obscures PDK2?
Check the no-primary section first; colour there implicates the detection workflow rather than primary-antibody recognition (standard IHC practice). Block endogenous peroxidase before HRP detection, and inspect pigment, folds, and section edges before treating brown deposits as cellular staining (standard chromogenic IHC practice). The selected image used 10% goat serum, 2 μg/ml primary antibody overnight at 4°C, and an HRP-linked secondary for 30 minutes at 37°C (caption A03261). If background persists, titrate the primary antibody and shorten DAB development on matched sections, preserving a known positive control to detect loss of useful signal (standard IHC practice).
How should I score PDK2 across samples with different cell composition? ⚠ ANSWER MARKED FOR VERIFICATION
Define the compartment and cell population before scoring: HPA reports ubiquitous cytoplasmic staining but different levels among annotated cell types (HPA tissue IHC). For comparable regions, record the percentage of positive cells and intensity or calculate an H-score, applying the same threshold and imaging settings to every section (standard IHC practice). Normalise positive-cell counts to the number of evaluable cells of the chosen type, or report positive-cell density per mm² of viable tissue when cell counts are impractical (standard IHC practice). Exclude necrosis, folds, and poorly preserved regions consistently, and retain control-section results with each staining batch (standard IHC practice).
How can I distinguish genuine PDK2 staining from artefact?
A credible signal fits cytoplasmic staining with mitochondrial localisation, while a nuclear-only call needs caution because HPA rates nucleoplasmic localisation uncertain (HPA tissue IHC; HPA subcellular). Compare cell identity as well as colour: HPA reports high staining in adrenal gland glandular cells but no detection in soft-tissue fibroblasts, illustrating why adjacent cell populations should not share an assumed score (HPA tissue IHC). Strong colour confined to section edges or necrotic regions warrants review of morphology and processing controls (standard IHC practice). If a no-primary section develops DAB colour, investigate endogenous peroxidase or detection-related background before interpreting that colour as PDK2 (standard chromogenic IHC practice).
Boster reagents
Best PDK2 / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial IHC Antibodies
A03261 has IHC images from human paraffin-embedded breast and lung cancer sections (A03261 IHC captions); PA1994 has an IF image from A549 cells (PA1994 IF caption).
Real IHC data
Anti-PDK2 Antibody ®
Cat # A03261
Real IF data
Anti-PDK2 Antibody ®
Cat # PA1994
A03261 will render with a human breast cancer section IHC figure; its catalog also documents IHC in human lung cancer sections and IF in U2OS cells (A03261 image captions). PA1994 will render with an A549 cell IF figure and is listed for IF/ICC (PA1994 IF caption and applications).
Which to pick: For tissue IHC, choose A03261: its rabbit antibody is listed for IHC and shown in paraffin-embedded human sections after EDTA pH 8 retrieval; the fixative is unreported (A03261 catalog applications and IHC captions). For IF/ICC, choose PA1994, a rabbit antibody shown in A549 cells at 5 μg/ml (PA1994 catalog applications and IF caption). For cross-species work, both list Human, Mouse and Rat reactivity, while the supplied tissue IHC images document human sections only (A03261 and PA1994 catalog reactivity; A03261 IHC captions).
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 Observed cytoplasmic staining; mitochondrial matrix expected (HPA tissue IHC; 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 conditions consistent across sections. (standard IHC practice; not target-specific); Caveat: Staining and RNA expression show medium consistency (HPA tissue IHC); Isoform / epitope: Two isoforms; epitope coverage is 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.