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- Table of Contents
Plan chromogenic IHC for NKX2-1 around nuclear staining in thyroid glandular and lung alveolar type I cells (HPA tissue IHC). Use adrenal glandular cells, where staining was not detected, as a comparison and keep fixation consistent across sections (HPA tissue IHC; standard IHC practice).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear staining in thyroid and lung (HPA tissue IHC) | |
| Staining pattern | Strong nuclear staining in thyroid glandular and lung alveolar type I cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M01322-3) | |
| Positive control | Lung+3 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation conditions consistent across paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Bronchial and nasopharyngeal epithelium also stains (HPA tissue IHC) | |
| Regulation | Thyroid and lung enriched expression (HPA tissue IHC) | |
| Isoform / epitope | 2 isoforms; antibody epitope coverage is unknown (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet: M01322-3) is followed by four published NKX2-1 chromogenic IHC protocols (PMC2950211; PMC6541221; PMC2705775; PMC6138525).
| Sample | Paraffin-embedded human thyroid cancer tissue; fixative not specified (datasheet M01322-3) |
| Fixation | Image fixative and duration unreported (datasheet M01322-3); 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 M01322-3); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M01322-3) |
| Primary antibody | Rabbit monoclonal (clone 27N58) anti-NKX2-1, 1:50-1:200 (datasheet M01322-3) |
| Primary incubation | Overnight at 4 °C (datasheet M01322-3) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M01322-3) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | NKX2-1-positive staining in alveolar cells type I of lung (HPA tissue IHC: High). HPA tissue profile: Selective nuclear expression in thyroid and lung. No signal in the no-primary control. |
NKX2-1 is a nuclear transcription factor with no transmembrane segment (UniProt P43699: localization, topology). In paraffin-section IHC, expect selective nuclear staining in thyroid glandular cells and lung alveolar type I cells, with weaker staining in respiratory epithelium of bronchus and nasopharynx (HPA tissue IHC: high in thyroid and lung; medium in bronchus and nasopharynx). HPA rates its tissue pattern Enhanced, reflecting high consistency between staining and RNA expression (HPA tissue IHC: reliability).
| Strong, discrete nuclear chromogen in thyroid glandular cells or lung alveolar type I cells. | This matches the reported high-staining populations and nuclear pattern (HPA tissue IHC: thyroid and lung high, selective nuclear expression). Judge the cells and their nuclei, rather than treating any brown tissue area as a positive result (standard IHC practice). |
| Predominantly cytoplasmic, membranous, or diffuse extracellular color, with little nuclear signal. | This conflicts with the expected nuclear location and absence of a transmembrane segment (UniProt P43699: localization, topology). Treat it as suspect staining; examine background and controls before assigning it to NKX2-1 (standard IHC practice). |
| Prominent staining in adipocytes or adrenal glandular cells, especially outside nuclei. | HPA reports NKX2-1 as not detected in these populations (HPA tissue IHC: adipose tissue and adrenal gland). Consider cross-reactivity or endogenous chromogenic activity, then check whether the same staining appears in a no-primary control (standard IHC practice). |
| A general haze or widespread brown color obscures cell boundaries and nuclei. | This cannot establish the selective nuclear pattern reported by HPA (HPA tissue IHC: profile). Nonspecific reagent binding, residual detection activity, or insufficient washing can produce background; compare the negative control and inspect whether the signal is confined to nuclei (standard IHC practice). |
| No nuclear signal in thyroid glandular cells or lung alveolar type I cells. | A blank known-positive population conflicts with HPA's high staining observations (HPA tissue IHC: thyroid and lung high). First verify tissue identity and an intact staining run; then review retrieval, primary antibody use, and detection steps as general IHC checks (standard IHC practice). |
| Tissue and cell selection | Thyroid glandular cells and lung alveolar type I cells provide HPA-reported high examples; bronchial and nasopharyngeal respiratory epithelial cells are medium (HPA tissue IHC). Interpret a weaker respiratory epithelial result against its own reported level, rather than expecting every positive site to match thyroid or lung (HPA tissue IHC: positive populations). |
| Antibody evidence for IHC | HPA lists CAB000078 and CAB053633 as IHC Enhanced; that designation reflects reproduced staining by independent antibodies or orthogonal data (HPA antibodies: IHC validation). It supports use of the reported tissue pattern as a benchmark, while slide-level controls remain necessary to assess a particular staining run (standard IHC practice). |
| Isoforms and epitope coverage | UniProt lists two NKX2-1 isoforms, 1 and 3 (UniProt P43699: isoforms). The supplied record gives no antibody epitope or isoform recognition data, so a difference between specimens cannot be assigned to isoform coverage from these sources alone (UniProt P43699: isoforms; HPA antibodies: validation fields). |
| Antigen retrieval, as a general IHC variable | If a known-positive paraffin section is blank, review the retrieval step alongside the primary and detection steps (standard IHC practice). The supplied HPA tissue pattern and UniProt record do not establish an NKX2-1-specific retrieval requirement or a fixation effect (HPA tissue IHC: scope; UniProt P43699: record). |
| IF/ICC: should the same compartment be expected? | For this IHC guide, use the selective nuclear tissue pattern (HPA tissue IHC: profile; UniProt P43699: nucleus). HPA's separate ICC-IF entry reports Golgi apparatus and vesicles as uncertain in its imaged cell lines (HPA subcellular: uncertain locations, HEK293, U-251MG, U2OS). That entry does not override the tissue IHC benchmark (HPA tissue IHC: profile). |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive thyroid or lung section is blank. | The observed result conflicts with HPA-reported high staining; the source does not identify a specific failed step (HPA tissue IHC: thyroid and lung high). | Confirm the scored cell population, then check retrieval, primary antibody, chromogen, and run controls in sequence (standard IHC practice). |
| Color is mainly cytoplasmic or membranous. | That compartment conflicts with NKX2-1's nuclear annotation and lack of a transmembrane segment (UniProt P43699: localization, topology). | Inspect nuclear counterstain and a no-primary control; review blocking, washing, and detection if extranuclear color persists (standard IHC practice). |
| Adipocytes or adrenal glandular cells appear strongly positive. | HPA reports NKX2-1 as not detected in those cells; cross-reactivity or endogenous detection activity is possible (HPA tissue IHC: negative populations; standard IHC practice). | Compare a no-primary control and reassess whether signal is nuclear; investigate detection background before scoring it as NKX2-1 (standard IHC practice). |
| Diffuse brown background makes nuclei hard to distinguish. | Background can arise from nonspecific binding or residual chromogenic activity (standard IHC practice). It obscures HPA's selective nuclear pattern (HPA tissue IHC: profile). | Check the negative control, blocking, washes, and chromogen development; rescore only where individual nuclei are clearly resolved (standard IHC practice). |
| Bronchial or nasopharyngeal epithelium stains less intensely than thyroid. | HPA rates those respiratory epithelial populations medium, versus high thyroid glandular staining (HPA tissue IHC: positive populations). | Judge localization and the appropriate tissue reference before changing conditions solely to equalize intensity (HPA tissue IHC: nuclear profile and levels; standard IHC practice). |
| An ICC-IF image suggests Golgi or vesicle signal while the IHC slide is nuclear. | HPA marks those ICC-IF locations uncertain, while tissue IHC shows selective nuclear expression (HPA subcellular: uncertainty; HPA tissue IHC: profile). | Interpret the paraffin-section result against tissue IHC and its controls; consult the separate IF/ICC guide for that application's images (HPA tissue IHC: profile; HPA subcellular: ICC-IF). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High 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 |
|---|---|---|---|---|
| Lung | Alveolar cells type I | High | Protein (IHC) | HPA → |
| Thyroid gland | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
| Nasopharynx | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
Troubleshoot NKX2-1 staining in paraffin sections by checking retrieval, nuclear localisation, cell identity and controls (UniProt P43699; HPA tissue IHC).
IHC images cover human lung and thyroid tissue (catalog image captions); IF images cover human lung tissue and HeLa cells (catalog image captions). All three antibodies list human, mouse and rat reactivity (catalog applications/reactivity).
M01322-3 shows IHC in paraffin-embedded human thyroid cancer tissue, with EDTA retrieval at pH 8.0 (M01322-3 image caption). A01322 shows IHC and IF in human lung tissue (A01322 image captions), while M01322-1 shows IHC in paraffin-embedded human thyroid and IF in HeLa cells (M01322-1 image captions).
Which to pick: For paraffin-section IHC, choose M01322-3 when its documented EDTA retrieval workflow fits: its caption reports 1:50 primary antibody and DAB detection; the fixative is unreported (M01322-3 image caption). For IF/ICC, choose M01322-1, a rabbit monoclonal with IF and ICC listed and an IF image in HeLa cells (M01322-1 catalog applications; M01322-1 IF image caption). For work across human, mouse and rat, all three list reactivity with those species; their supplied IHC images show human samples, so verify staining in the intended species (catalog reactivity; catalog IHC image captions).