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- Table of Contents
This guide helps plan AIFM1 paraffin IHC around granular cytoplasmic tissue staining (HPA tissue IHC). It covers controls and scoring of cytoplasmic and nuclear signal, since apoptosis can move AIFM1 into nuclei (UniProt).
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); mitochondrial IMS expected (UniProt) | |
| Staining pattern | Generally granular cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet PB9366) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Apoptosis can shift staining toward nuclei (UniProt) | |
| Regulation | Apoptotic stimuli redistribute AIFM1 (UniProt) | |
| Isoform / epitope | Six isoforms; mature chain starts at residue 102—check epitope position (UniProt) |
Compare the catalog antibody's IHC-P protocol (datasheet: PB9366) with the published human HNSC tissue protocol (PMC12055095).
| Sample | Paraffin-embedded Rat Cardiac Muscle tissue; fixative not specified (datasheet PB9366) |
| Fixation | Image fixative and duration unreported (datasheet PB9366); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet PB9366) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PB9366) |
| Primary antibody | Rabbit anti-AIFM1, 0.5-1μg/ml (datasheet PB9366) |
| Primary incubation | Overnight at 4 °C (datasheet PB9366) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9366) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | AIFM1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: General granular cytoplasmic expression. No signal in the no-primary control. |
AIFM1 is chiefly mitochondrial, with an inner-membrane-anchored form in the intermembrane space (UniProt O95831 localization and processing). In paraffin-section IHC, expect granular cytoplasmic staining in selected cells, including pancreatic exocrine glandular cells and adrenal glandular cells with high HPA staining (HPA tissue IHC). HPA rates its tissue IHC evidence Enhanced, reflecting agreement between staining and RNA expression (HPA tissue IHC).
| Granular cytoplasmic staining in pancreatic exocrine glandular cells or adrenal glandular cells, with clearly defined cell outlines. | This matches HPA's general granular cytoplasmic profile and its High calls for those cells (HPA tissue IHC). Granularity is compatible with mitochondrial localization (UniProt O95831 localization); chromogenic IHC alone does not prove mitochondrial colocalization. |
| Predominantly nuclear staining in otherwise unremarkable cells, without a convincing granular cytoplasmic pattern. | Treat an isolated nuclear pattern cautiously: HPA describes general granular cytoplasmic tissue staining (HPA tissue IHC). AIFM1 can move from mitochondria to nuclei during apoptosis (UniProt O95831 localization and function), so nuclear staining needs biological context and independent confirmation before interpretation. |
| Strong staining in adipocytes or bone-marrow hematopoietic cells while a matched known-positive cell population stains weakly. | HPA reports those cell populations as Not detected (HPA tissue IHC). Review morphology and controls for cross-reactivity or endogenous detection activity (general IHC practice). A tissue-wide label must not replace a cell-specific reading. |
| Broad, diffuse color covers cells and surrounding tissue, obscuring granular cytoplasmic detail. | That appearance cannot establish the reported AIFM1 pattern (HPA tissue IHC). Check the no-primary control, blocking, washing and chromogen development for background (general IHC practice), then score only signal that can be assigned to identifiable cells. |
| No convincing signal in pancreatic exocrine glandular cells on an otherwise interpretable section. | These cells are High in HPA tissue IHC (HPA tissue IHC), so an absent result warrants a run-level check. Confirm tissue identity and preservation, then review the antibody dilution, retrieval, detection reagents and positive control (general IHC practice); absence alone does not show loss of AIFM1. |
| Cell population and tissue choice | HPA calls pancreatic exocrine and adrenal glandular cells High, colon glandular cells Low, and adipocytes Not detected (HPA tissue IHC). Compare named cell populations under the microscope; a negative call in one population does not characterize every cell in its tissue. |
| Mitochondrial processing and redistribution | AIFM1 forms an inner-membrane-anchored mature form and can yield a soluble form that moves to cytoplasm and nucleus during apoptosis (UniProt O95831 processing and localization). Interpret a changed compartment alongside morphology and an independent marker; location alone cannot identify the processed form. |
| Antibody evidence | HPA lists HPA030611 and CAB003764 as IHC Enhanced (HPA antibodies). That supports the reported tissue pattern; it does not establish that every staining event is specific. Include appropriate positive and no-primary controls when assessing a new IHC run (general IHC practice). |
| Isoform and epitope limits | UniProt lists 6 AIFM1 isoforms and a processed chain spanning residues 102–613 (UniProt O95831 isoforms and processing). The supplied antibody evidence does not locate either antibody's epitope (HPA antibodies); do not infer which isoforms or processed forms a stain detects. |
| IF/ICC Q&A: What pattern should I expect? | Mainly mitochondrial signal is the HPA ICC-IF finding; connecting-piece localization is additional (HPA subcellular ICC-IF). That supports a localization comparison, not an IF protocol or a claim that paraffin-section chromogenic granules resolve individual mitochondria. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive glandular cells appear unstained. | A failed IHC run or unsuitable section remains possible; pancreatic exocrine glandular cells are High in HPA tissue IHC (HPA tissue IHC). | Check tissue identity, section quality and the run's positive control; then review retrieval, catalog-antibody dilution and detection steps (general IHC practice). Do not assign an AIFM1-specific fixation effect from these data. |
| Color is widespread and granular detail is lost. | Nonspecific reagent binding, inadequate washing or excess chromogen development can produce background (general IHC practice). | Inspect the no-primary control and staining distribution. Adjust blocking, washes or detection conditions as indicated by that control (general IHC practice), then reassess the HPA granular cytoplasmic pattern (HPA tissue IHC). |
| An HPA Not detected cell population stains strongly. | For adipocytes or bone-marrow hematopoietic cells, this conflicts with the reported HPA cell-level call (HPA tissue IHC); cross-reactivity or endogenous detection activity is possible (general IHC practice). | Confirm cell identity, compare a positive population and inspect no-primary and detection controls before scoring the unexpected signal (general IHC practice). |
| Nuclear staining dominates the section. | AIFM1 nuclear translocation is linked to apoptosis (UniProt O95831 localization and function), but nuclear color alone does not establish that event. | Check cell morphology and controls, then seek independent evidence of apoptosis or localization before reporting redistribution (general IHC practice). Compare with HPA's granular cytoplasmic baseline (HPA tissue IHC). |
| A Low population stains less than a High population. | This can fit HPA's cell-level calls: colon glandular cells are Low and pancreatic exocrine glandular cells are High (HPA tissue IHC). | Score the named cell types separately and use the same scoring criteria across sections (general IHC practice). Avoid treating a weak Low population as a failed run when its positive control performs. |
| Granular cytoplasmic staining is present, but mitochondrial identity is uncertain. | HPA tissue IHC reports granularity, while mitochondrial localization comes from UniProt and HPA ICC-IF (HPA tissue IHC; UniProt O95831 localization; HPA subcellular ICC-IF). | Report the visible chromogenic pattern as granular cytoplasmic. If mitochondrial assignment matters, assess colocalization in a separately validated localization experiment (general IHC/IF practice). |
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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
| Fallopian tube | Glandular cells | High | Protein (IHC) | HPA → |
| Kidney | Bowman's capsule | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebral cortex | Endothelial cells | Not detected | Protein (IHC) | HPA → |
| Hippocampus | Glial cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot AIFM1 staining in paraffin sections by checking retrieval, cell type and compartment before interpreting chromogenic signal.
Anti-AIFM1 antibodies have IHC images from human, mouse, and rat tissues and IF images from cultured cells (catalog image captions).
PB9366 was imaged in rat cardiac muscle, M01571-1 in human mammary cancer, and PA2232 in human lung cancer paraffin sections (catalog IHC captions). M01571-4 has a mouse kidney IHC image, while M01571 has an IF image of HeLa cells (catalog image captions).
Which to pick: For paraffin-section IHC, choose PB9366 for rat cardiac muscle with citrate pH 6 retrieval or M01571-1 for human mammary cancer with EDTA pH 8 retrieval; neither caption reports the fixative (catalog IHC captions). For IF/ICC, M01571 lists both applications and has an IF image of HeLa cells (catalog applications and IF caption). For cross-species tissue IHC, M01571-4 lists human, mouse, and rat reactivity and has kidney IHC images from all three species (catalog reactivity and IHC captions).