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- Table of Contents
Plan chromogenic GFRA1 IHC in paraffin sections using the reported glandular-cell cytoplasmic pattern (HPA tissue IHC). Interpret positive staining cautiously because its agreement with RNA expression is very low (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasm in tissue IHC (HPA tissue IHC); mainly plasma membrane molecularly (UniProt) | |
| Staining pattern | Glandular cells show cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet PB9202) | |
| Positive control | Appendix+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 | Staining has very low concordance with RNA expression (HPA tissue IHC) | |
| Regulation | Expression regulation is unreported (UniProt) | |
| Isoform / epitope | 2 isoforms; mature chain spans residues 25–429; verify epitope (UniProt) |
The catalog antibody protocol uses EDTA pH 8.0 retrieval (PB9202 datasheet). The published protocols below describe chromogenic GFRA1 staining in rat testis and human breast tumors (PMC12670479; PMC11937365).
| Sample | Paraffin-embedded human lung cancer tissue; fixative not specified (datasheet PB9202) |
| Fixation | Image fixative and duration unreported (datasheet PB9202); 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 PB9202); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PB9202) |
| Primary antibody | Rabbit anti-GFRA1, 0.5-1μg/ml (datasheet PB9202) |
| Primary incubation | Overnight at 4 °C (datasheet PB9202) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9202) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | GFRA1-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in several tissues. No signal in the no-primary control. |
GFRA1 is mainly at the plasma membrane, with vesicular localisation under some conditions; it has no transmembrane segment (UniProt P56159 topology and subcellular annotation). In tissue IHC, HPA reports cytoplasmic staining in several tissues, including high staining in appendix, duodenum and rectum glandular cells (HPA tissue IHC). Treat that pattern as provisional: HPA rates the tissue staining Uncertain because antibody staining and RNA expression show very low consistency (HPA tissue IHC).
| Glandular cells stain strongly in appendix, duodenum or rectum, with a discernible cell-associated signal (HPA: High in those cells). | This matches the reported tissue IHC pattern, which HPA describes as cytoplasmic (HPA tissue IHC). Assess the stained cells against adjacent tissue and controls before calling them GFRA1-positive: HPA rates the IHC pattern Uncertain, so a matching location and intensity alone do not establish antibody specificity (HPA tissue IHC). |
| A cell-associated membrane outline or intracellular puncta appear in a stained cell. | These compartments are biologically plausible: GFRA1 localises mainly to the plasma membrane and can shift into trans-Golgi and endosomal vesicles in the presence of SORL1 (UniProt P56159 subcellular annotation). HPA's tissue IHC summary instead reports cytoplasmic staining, so compare the pattern with the tissue control; do not require crisp membrane staining in every paraffin section (HPA tissue IHC; UniProt P56159). |
| Staining is predominantly nuclear, or appears in a compartment that cannot be distinguished from background. | Reassess it as a possible artefact in tissue IHC: HPA's tissue summary is cytoplasmic, while UniProt places GFRA1 mainly at the membrane and also in vesicular compartments (HPA tissue IHC; UniProt P56159). A nuclear IF observation cannot by itself validate nuclear IHC: HPA separately reports approved nucleoplasmic staining in ICC-IF (HPA subcellular ICC-IF). |
| Strong staining appears in an HPA-listed undetected cell population, such as adipocytes in adipose tissue or respiratory epithelium in bronchus (HPA tissue IHC). | Check for antibody cross-reactivity or endogenous detection activity before assigning a GFRA1-positive result (general IHC practice). The HPA comparison is cell-specific: its 'Not detected' entries refer to the listed cells and sampled staining, not a guarantee that every cell in that organ lacks GFRA1 (HPA tissue IHC). |
| Diffuse colour covers cells and surrounding tissue, or no signal appears in appendix, duodenum or rectum glandular cells. | Diffuse signal weakens localisation and may reflect background from blocking, detection or overdevelopment; a blank reported-positive control may reflect assay failure or variable tissue staining (general IHC practice; HPA: High in the listed glandular cells). Neither outcome alone proves GFRA1 absence or presence, especially given HPA's Uncertain tissue IHC rating (HPA tissue IHC). |
| Tissue and cell choice | HPA reports High glandular-cell staining in appendix, duodenum and rectum, Medium staining in colon, endometrium and gallbladder glandular cells, and Not detected staining in selected cell populations (HPA tissue IHC). Select controls by the named cell population, and interpret them provisionally because HPA rates the tissue pattern Uncertain (HPA tissue IHC). |
| Topology and trafficking | GFRA1 has no transmembrane segment and carries a GPI-anchor keyword; UniProt places it mainly at the plasma membrane but describes SORL1-associated internalisation into trans-Golgi, endosomal and multivesicular compartments (UniProt P56159). This supports assessing both cell-surface and intracellular patterns without claiming that either must dominate a given IHC section. |
| Processing and antibody epitope | UniProt annotates a signal peptide at residues 1–24, a mature chain at 25–429 and a propeptide at 430–465 (UniProt P56159 processing). The supplied record gives no antibody epitope, so these annotations cannot predict whether the IHC antibody recognises a processed form; check its documented immunogen or epitope before drawing that conclusion. |
| IF/ICC pattern? | HPA reports Golgi as the main approved ICC-IF location and nucleoplasm as an additional approved location, with images in MCF-7, U-251MG and U2OS (HPA subcellular ICC-IF). This is context for interpreting an IF image, not an IF protocol or proof that the same compartments should dominate paraffin-section IHC (HPA subcellular ICC-IF; HPA tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in appendix, duodenum or rectum glandular cells (HPA: High). | The IHC run may have failed, or the selected section may differ from the reported HPA pattern (general IHC practice; HPA tissue IHC, Uncertain). | Review tissue identity, cell type, antibody exposure, retrieval, detection and a working run control; adjust one general IHC step at a time. Do not infer a GFRA1-specific retrieval requirement from the supplied sources. |
| Weak signal in colon, endometrium, gallbladder, heart or kidney. | Medium is the reported HPA level in the specified glandular cells, cardiomyocytes or tubular cells, respectively (HPA tissue IHC). | Score the named cell population against the slide's background and a stronger reported-positive control. Avoid treating a Medium HPA entry as an expected High-intensity result (HPA tissue IHC). |
| Strong colour appears across most structures, including spaces between cells. | Nonspecific detection, inadequate blocking or excessive chromogen development can obscure cell-associated staining (general IHC practice). | Compare a negative reagent control and the reported-positive tissue; then review blocking, detection and development settings (general IHC practice). Retain only a cell-associated pattern as interpretable. |
| Strong staining appears in an HPA-listed Not detected cell type. | Possible cross-reactivity or endogenous detection activity; HPA's tissue IHC assessment is Uncertain (general IHC practice; HPA tissue IHC). | Check the listed cell identity, negative reagent control and detection chemistry. Seek independent validation before calling unexpected staining GFRA1-specific (general IHC practice; HPA tissue IHC, Uncertain). |
| An apparently nuclear-only IHC pattern conflicts with the expected tissue pattern. | HPA reports cytoplasmic tissue IHC, although its separate ICC-IF dataset also reports approved nucleoplasmic localisation (HPA tissue IHC; HPA subcellular ICC-IF). | Compare cell-associated cytoplasmic signal and negative controls on the IHC slide. Report nuclear staining as unresolved unless independently validated in that tissue and method; do not transfer the ICC-IF call directly to IHC. |
| A section shows puncta rather than a crisp cell-surface outline. | Intracellular localisation is plausible when SORL1 promotes GFRA1 internalisation (UniProt P56159 subcellular annotation), but puncta alone do not establish that mechanism. | Assess whether puncta are confined to the expected cells and exceed background; compare the reported-positive tissue and controls (HPA tissue IHC; general IHC practice). Describe the observed compartment without claiming SORL1 activity. |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Very low consistency between antibody staining and RNA expression data. Pending external verification.). 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 |
|---|---|---|---|---|
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Rectum | Glandular cells | High | Protein (IHC) | HPA → |
| Colon | Glandular cells | Medium | Protein (IHC) | HPA → |
| Endometrium | Glandular 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 → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
Troubleshoot GFRA1 chromogenic IHC in paraffin sections using the selected antibody’s tissue image, protein annotations, and cautious interpretation of tissue staining.
Validated anti-GFRA1 antibodies have IHC images from human lung cancer and brain tissue, plus a human brain IF image (PB9202 IHC caption; A02897 IHC/IF captions).
PB9202 is listed for human IHC and has a paraffin-section image from human lung cancer tissue (PB9202 applications/reactivity; PB9202 IHC caption). A02897 is listed for human, mouse and rat IHC-P and IF, with IHC and IF images from human brain tissue (A02897 applications/reactivity; A02897 IHC/IF captions).
Which to pick: Choose PB9202 for human tissue IHC when its documented paraffin-section workflow is useful: EDTA retrieval at pH 8.0 and 1 μg/ml primary antibody overnight at 4°C (PB9202 IHC caption). Choose A02897 for IF or work involving mouse or rat, based on its listed applications and reactivity; its IF image is from human brain tissue, while ICC validation and clonality are unreported (A02897 applications/reactivity; A02897 IF caption; catalog clone field). The fixative is unreported for both IHC images (PB9202 IHC caption; A02897 IHC captions).