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- Table of Contents
Plan PDHA1 staining in paraffin sections using the granular cytoplasmic tissue pattern (HPA tissue IHC) and mitochondrial matrix location (UniProt) to set expectations. This guide covers fixation consistency, chromogenic detection and scoring by cell type.
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Tissue: granular cytoplasm (HPA tissue IHC); PDHA1: mitochondrial matrix (UniProt) | |
| Staining pattern | Granular cytoplasmic staining in most cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A01906-4) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
| Fixation | Keep fixation consistent across paraffin-section comparison groups. (selected-SKU IHC image A01906-4) | |
| Caveat | HPA staining may detect protein from more than one gene (HPA tissue IHC) | |
| Regulation | Muscle/tongue RNA is tissue-enhanced (HPA tissue RNA) | |
| Isoform / epitope | 4 isoforms; map the antibody epitope across them (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet: A01906-4) is accompanied by two published prostate cancer section protocols (PMC12949121; PMC5355102).
| Sample | Paraffin-embedded human appendix carcinoid tissue; fixative not specified (datasheet A01906-4) |
| Fixation | Image fixative and duration unreported (datasheet A01906-4); 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 A01906-4); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A01906-4) |
| Primary antibody | Rabbit anti-PDHA1, 1:50 recommended; image 1:100 (datasheet A01906-4) |
| Primary incubation | Overnight at 4 °C (datasheet A01906-4) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A01906-4) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PDHA1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Granular cytoplasmic expression in most cell types. No signal in the no-primary control. |
PDHA1 localises to the mitochondrial matrix and has no transmembrane segment (UniProt P08559). In paraffin sections, expect granular cytoplasmic staining in most cell types, with high staining in several glandular and neuronal populations (HPA: tissue IHC). HPA rates the tissue pattern Approved, reports medium agreement with RNA data, and cautions that its staining evidence includes antibodies targeting proteins from more than one gene (HPA: tissue IHC).
| Granular cytoplasmic stain in adrenal gland or breast glandular cells, or in cerebral cortex neurons (HPA: High in these cells). | This fits the reported tissue pattern and a mitochondrial matrix protein (HPA: granular cytoplasmic expression; UniProt P08559). Judge the granules within identified cells, allowing unstained nuclei and differences in staining between cell populations (general IHC practice). |
| Predominantly nuclear, membranous or extracellular stain, with little granular cytoplasmic signal. | Those compartments do not match PDHA1's matrix location or HPA's tissue pattern (UniProt P08559; HPA: tissue IHC). Treat the result as suspect and review controls and morphology before assigning it to PDHA1 (general IHC practice). |
| Strong staining mainly in alveolar cells, adipocytes or chondrocytes, while an expected high-staining population is weak (HPA: Low versus High cells). | This reversal warrants a specificity check; HPA reports Low staining in those populations and cautions about antibodies targeting multiple genes (HPA: tissue IHC). Broad PDHA1 expression means staining outside the High list is not automatically false (UniProt: ubiquitous). |
| Diffuse stain covers cells and surrounding section without discernible cytoplasmic granules. | The appearance does not reproduce HPA's granular cytoplasmic pattern (HPA: tissue IHC). Review nonspecific antibody staining and chromogen background with appropriate controls; a uniform haze cannot establish the intracellular compartment (general IHC practice). |
| No staining in adrenal gland glandular cells or cerebral cortex neurons that are identifiable on the section (HPA: High). | A negative result there conflicts with the reported High staining, but alone cannot distinguish a technical failure from antibody specificity or specimen variation (HPA: tissue IHC; general IHC practice). Review a known-positive control before scoring the specimen negative. |
| Compartment and tissue context (UniProt P08559; HPA: tissue IHC) | PDHA1 is a matrix protein with no transmembrane segment; HPA describes granular cytoplasmic staining in most cell types. Use cell morphology to assign colour to cytoplasm rather than to adjacent structures (UniProt P08559; HPA: tissue IHC; general IHC practice). |
| Expression range (UniProt: ubiquitous; HPA: tissue IHC) | HPA lists High staining in selected glandular and neuronal cells and Low staining in alveolar cells, adipocytes and chondrocytes. These are relative reference patterns, so Low is not a negative control and an unlisted cell type has no assigned HPA level here (HPA: tissue IHC). |
| Antibody evidence (HPA: tissue IHC; HPA: antibodies) | Three listed antibodies have Approved IHC status, while HPA reports medium agreement with RNA data and cautions about multi-gene targeting. An expected pattern supports interpretation but does not by itself prove PDHA1-specific binding (HPA: tissue IHC; HPA: antibodies). |
| Mature chain, isoforms and modifications (UniProt P08559) | UniProt lists a mature chain at residues 30–390, four isoforms and modified residues including phosphorylation and acetylation. The supplied evidence does not locate the catalog antibody's epitope, so its response to those sequence or modification differences is unknown (UniProt P08559). |
| IF/ICC: where should signal appear? (HPA: subcellular ICC-IF) | HPA supports a mainly mitochondrial location in ICC-IF, consistent with UniProt's matrix assignment. HPA also cautions that this localisation evidence uses antibodies targeting proteins from multiple genes; interpret it as localisation guidance for the separate IF/ICC guide (HPA: subcellular ICC-IF; UniProt P08559). |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive glandular or neuronal tissue lacks stain (HPA: High in listed cells). | The result does not match HPA's reported pattern; the staining run or specimen may have failed (HPA: tissue IHC; general IHC practice). | Check a known-positive section processed in the same run, then review retrieval and detection steps against the IHC-validated antibody's instructions before interpreting a negative specimen (general IHC practice). |
| Nuclei stain more strongly than cytoplasmic granules. | Predominantly nuclear colour conflicts with the expected matrix location and granular cytoplasmic pattern (UniProt P08559; HPA: tissue IHC). | Compare with a no-primary control and inspect cell boundaries and counterstain; score only convincing cytoplasmic signal as the expected pattern (general IHC practice). |
| Broad brown haze obscures tissue detail. | Diffuse background prevents assessment of HPA's granular pattern; nonspecific staining or detection background is possible (HPA: tissue IHC; general IHC practice). | Compare a no-primary control, review blocking and washes, and adjust detection conditions according to the validated IHC workflow (general IHC practice). |
| Colour appears in the no-primary control. | Primary-antibody binding cannot explain colour in that control; endogenous activity or detection reagents may contribute (general IHC practice). | Review the chromogenic detection controls and the applicable endogenous-activity blocking step before attributing tissue colour to PDHA1 (general IHC practice). |
| Low-reference cells are strongly stained while High-reference cells are faint (HPA: tissue IHC). | The reversal may reflect assay or specificity problems; HPA cautions that its evidence includes multi-gene targeting (HPA: tissue IHC). | Check tissue identity and morphology, compare an expected High population on the same run, and seek independent antibody evidence before calling the reversed pattern PDHA1-specific (HPA: tissue IHC; general IHC practice). |
| A section has sparse staining in cell types outside HPA's High list. | PDHA1 is described as ubiquitous, while HPA reports different staining levels across cell types; sparse signal alone is inconclusive (UniProt P08559; HPA: tissue IHC). | Score the identified cell population and intracellular pattern against the available HPA reference; avoid treating HPA Low cells as absolute negatives (HPA: tissue IHC; general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data. Caution, targets protein from more than one gene.). 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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Caudate | Neuronal cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: PDHA1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot PDHA1 chromogenic IHC by checking retrieval, staining pattern and controls before comparing signal across sections.
Anti-PDHA1 antibodies have IHC images from human tissue and human, mouse, and rat kidney (catalog image captions), plus an IF/ICC image from HeLa cells (A01906-3 image caption).
A01906-4 shows IHC staining of human paraffin sections, including appendix carcinoid tissue (A01906-4 image caption); M01906-2 shows IHC staining of rat, human, and mouse kidney (M01906-2 image captions). A01906-3 shows IF/ICC staining in HeLa cells (A01906-3 image caption) and lists IHC and IF among its applications (catalog applications).
Which to pick: For human paraffin-section IHC, choose A01906-4: its image caption documents EDTA retrieval at pH 8.0 and chromogenic DAB detection; the fixative is unreported (A01906-4 image caption). For IF/ICC, choose A01906-3: its HeLa image documents paraformaldehyde fixation and 0.25% Triton X100/PBS permeabilisation (A01906-3 image caption). For kidney IHC across human, mouse, and rat, choose the rabbit monoclonal M01906-2, which has an IHC image for each species; the captions do not report tissue processing or fixative (catalog description; M01906-2 image captions).