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- Table of Contents
Plan ALK chromogenic IHC in paraffin sections using cerebellar Purkinje cells, which show high staining, as a positive reference (HPA tissue IHC). Compare the expected membrane location (UniProt) with observed cytoplasmic and nuclear tissue staining, and assess possible off-target binding (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Membrane expected (UniProt); cytoplasm and nuclei observed (HPA tissue IHC) | |
| Staining pattern | Neurons show cytoplasmic and nuclear staining (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Cerebellum+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Presumed off-target binding may mimic ALK staining (HPA tissue IHC) | |
| Regulation | Transient in select neural regions (UniProt) | |
| Isoform / epitope | No isoforms listed; extracellular versus cytoplasmic epitope matters (UniProt) |
The catalog antibody protocol is accompanied by one published ALK IHC method using FFPE tissue sections (PMC5890087).
| Sample | Tissue sections; selected-image fixative not specified (standard IHC workflow) |
| Fixation | Image fixative and duration unreported (datasheet M00301-5); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit anti-ALK, 1:200-1:1000 (datasheet M00301-5) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ALK-positive staining in purkinje cells of cerebellum (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic and nuclear expression in several different tissue types, most abundant in neurons. No signal in the no-primary control. |
ALK is a single-pass cell-membrane receptor with an extracellular region and a cytoplasmic kinase region (UniProt Q9UM73 topology). In IHC, the strongest reported staining is in cerebellar Purkinje cells and neurons of the cerebral cortex and hippocampus (HPA: High). HPA also reports cytoplasmic and nuclear tissue staining, but rates tissue IHC Approved with low agreement between staining and RNA data and notes presumed off-target binding (HPA: tissue IHC reliability).
| Distinct staining in Purkinje cells or cortical and hippocampal neurons, with staining at the cell edge and possibly within the cell (HPA: High in these cells; HPA: tissue profile). | This is the most persuasive tissue pattern for ALK IHC. Membrane staining fits receptor topology, while cytoplasmic staining has also been reported in tissue sections (UniProt Q9UM73 topology; HPA: tissue profile). Interpret intensity alongside cell identity and the negative control; HPA's Approved rating does not resolve its reported staining–RNA disagreement (HPA: tissue IHC reliability; general IHC practice). |
| Predominantly nuclear staining, especially without a discernible neuronal or membrane-associated pattern (HPA: tissue profile; UniProt Q9UM73 subcellular location). | Do not treat nuclear signal alone as proof of correctly localized ALK. HPA reports nuclear staining in tissue IHC, whereas UniProt assigns ALK to the cell membrane and HPA ICC-IF supports plasma-membrane localization (HPA: tissue profile; UniProt Q9UM73 subcellular location; HPA: subcellular). Review the full cell pattern and controls before assigning specificity (general IHC practice). |
| Strong staining in an unexpected cell population, such as adipocytes or pancreatic exocrine glandular cells (HPA: Not detected in those cells). | Compare the exact cell type rather than labeling the whole organ positive or negative: HPA reports no detection in these specified populations and presumed off-target tissue binding (HPA: tissue IHC; HPA: tissue IHC reliability). Cross-reactivity or endogenous chromogen-generating activity should be considered if the signal also appears in appropriate controls (general IHC practice). |
| Diffuse color across many cell types, tissue spaces, or the section background, with little separation between neurons and surrounding tissue (general IHC practice). | That distribution provides weak evidence for cell-specific ALK staining. Check whether the same color appears in a no-primary control, then assess blocking, washing, detection reagents, and antibody concentration as general chromogenic IHC variables (general IHC practice). HPA's reported off-target binding adds a reason to require convincing cellular contrast (HPA: tissue IHC reliability). |
| No visible staining in Purkinje cells or cortical or hippocampal neurons on a section expected to contain them (HPA: High in these cells). | First verify that the relevant cells are present and preserved, then check the antibody's documented IHC-P procedure, detection reagents, and a concurrently processed positive control (general IHC practice). Absence of signal can reflect assay failure or sample variation; HPA's High observations do not establish that every section must stain identically (HPA: tissue IHC). |
| Cell and tissue selection (HPA: tissue IHC; UniProt Q9UM73 tissue specificity). | Cerebellar Purkinje cells and cerebral cortical and hippocampal neurons are reported High, while caudate neurons and skin keratinocytes are Medium (HPA: tissue IHC). UniProt reports expression in brain and CNS, small intestine, and testis, and absence from normal lymphoid cells; these are expression statements, not guaranteed IHC results in every specimen (UniProt Q9UM73 tissue specificity). |
| Antibody validation and interpretation (HPA: HPA010694 validation; HPA: tissue IHC reliability). | HPA010694 is Approved for IHC and Supported for ICC, but HPA describes low consistency between tissue staining and RNA expression and disregarded presumed off-target binding (HPA: antibody validation; HPA: tissue IHC reliability). Treat a positive tissue stain as evidence to assess with morphology and controls, not as independent confirmation of target identity (general IHC practice). |
| Compartment and epitope position (UniProt Q9UM73 topology; HPA: subcellular). | Full-length ALK has extracellular residues 19–1038, a transmembrane segment at 1039–1059, and cytoplasmic residues 1060–1620 (UniProt Q9UM73 topology). HPA ICC-IF supports plasma-membrane localization, while HPA tissue IHC describes cytoplasmic and nuclear staining (HPA: subcellular; HPA: tissue profile). The antibody epitope is unspecified here, so a domain-specific staining prediction cannot be made. |
| Antigen retrieval and detection settings (general IHC practice). | Use the chosen IHC-validated antibody's documented paraffin-section procedure and compare retrieval, antibody concentration, and chromogenic detection against controls when optimizing the assay (general IHC practice). Neither supplied source gives a target-specific retrieval condition or shows that fixation alters ALK epitope access or sensitivity; do not infer one from topology or HPA staining levels (UniProt Q9UM73; HPA: tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in an identifiable Purkinje-cell or cortical-neuron positive control (HPA: High in those cells). | The assay may have failed, or the relevant cells or antigen may be poorly represented in that section (general IHC practice). | Confirm morphology and control labeling, then review the documented IHC-P procedure, retrieval step, primary-antibody preparation, and detection reagents (general IHC practice). Do not infer an ALK-specific fixation effect from this result. |
| Neurons stain, but the entire section is similarly brown (HPA: High in selected neurons; general IHC practice). | Poor signal separation may arise from nonspecific antibody binding, insufficient washing, or detection background (general IHC practice); HPA also reports presumed off-target tissue binding (HPA: tissue IHC reliability). | Inspect a no-primary control, wash and block according to the assay protocol, and optimize antibody concentration using neuronal and low-signal cell populations on the same run (general IHC practice; HPA: tissue IHC). |
| An unexpected population stains more strongly than the reported neuronal positives (HPA: High in Purkinje and cortical or hippocampal neurons). | Cell-type misidentification or off-target staining is possible; HPA's tissue reliability note specifically records presumed off-target binding (HPA: tissue IHC reliability; general IHC practice). | Recheck morphology and the exact HPA cell-level comparison. For example, HPA reports adipocytes and pancreatic exocrine glandular cells as Not detected (HPA: tissue IHC). Compare controls before interpreting the unexpected population as ALK positive (general IHC practice). |
| Signal is chiefly nuclear, with little cell-edge staining (HPA: tissue profile; UniProt Q9UM73 subcellular location). | HPA has observed nuclear tissue staining, but the receptor's annotated location and supported ICC-IF location are at the membrane; nuclear signal alone leaves specificity uncertain (HPA: tissue profile and subcellular; UniProt Q9UM73 subcellular location). | Assess whether the same cells show a coherent neuronal pattern, compare the no-primary control, and report nuclear staining as an observation rather than definitive ALK localization (HPA: tissue profile; general IHC practice). |
| Chromogen appears in the no-primary control (general IHC practice). | The color can come from endogenous detection activity or the detection system rather than primary-antibody recognition (general chromogenic IHC practice). | Address the control-positive step in the detection workflow, including appropriate endogenous-activity blocking where applicable, before scoring ALK staining (general chromogenic IHC practice). |
| IHC tissue staining seems inconsistent with membrane-focused IF images (HPA: tissue profile; HPA: subcellular). | The source observations come from different applications: HPA tissue IHC reports cytoplasmic and nuclear expression, while its ICC-IF summary supports plasma-membrane localization (HPA: tissue IHC; HPA: subcellular). | Interpret each assay against its own controls and documented localization. Use the separate IF/ICC guide for IF setup; an ICC-supported antibody designation does not supply an IF protocol for this paraffin IHC guide (HPA: antibody validation; general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data. Presumed off target binding observed and disregarded.). 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 |
|---|---|---|---|---|
| Cerebellum | Purkinje cells | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Hippocampus | Neuronal cells | High | Protein (IHC) | HPA → |
| Caudate | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Skin | Keratinocytes | Medium | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Esophagus | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot ALK staining in paraffin sections by checking retrieval, antibody specificity, expected cell populations and subcellular pattern before scoring chromogenic signal.
The catalog lists human-reactive ALK antibodies for IHC and IF; one also lists mouse and rat reactivity (catalog: applications and reactivity). The supplied figures show IHC staining only (catalog: image captions).
M00301-5 lists human IHC and IF applications and shows IHC staining of human non-Hodgkin lymphoma and neuroblastoma (catalog: applications, reactivity, IHC image captions). M00301-3 lists human, mouse and rat IHC, ICC and IF applications; its IHC figure shows a paraffin-embedded human kidney section (catalog: applications, reactivity, IHC image caption).
Which to pick: For human tissue IHC, choose M00301-5 when lymphoma or neuroblastoma staining is relevant (M00301-5: IHC image captions); choose M00301-3 for a paraffin-section example in human kidney (M00301-3: IHC image caption). For IF/ICC or listed mouse and rat reactivity, choose M00301-3 (M00301-3: applications and reactivity); its supplied figure supports paraffin-section IHC, and the fixative is unreported (M00301-3: IHC image caption).