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- Table of Contents
Plan chromogenic ACLY IHC in paraffin sections around the cytoplasmic and nuclear staining seen across tissues (HPA tissue IHC). Pancreatic endocrine cells provide a high staining reference (HPA tissue IHC); the catalog antibody PB10024 has an IHC working range of 1–2 µg/mL (datasheet: PB10024).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasmic and nuclear tissue staining (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic/nuclear signal; pancreatic endocrine cells stain high (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet PB10024) | |
| Positive control | Pancreas+4 more · see all | |
| Negative control | Esophagus+4 more · see all |
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific). Selected-image fixative and duration unreported (datasheet PB10024); verify before use. | |
| Caveat | Antibody staining has low concordance with RNA expression (HPA tissue IHC) | |
| Regulation | No expression regulator annotated (UniProt) | |
| Isoform / epitope | 3 isoforms; epitope coverage is unresolved (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet: PB10024) is accompanied by published ACLY staining protocols for lung cancer (PMC4427316) and mouse xenograft sections (PMC6774899).
| Sample | Paraffin-embedded human colonic adenocarcinoma tissue; fixative not specified (datasheet PB10024) |
| Fixation | Image fixative and duration unreported (datasheet PB10024); 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 PB10024); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PB10024) |
| Primary antibody | Rabbit anti-ACLY, 1-2μg/ml (datasheet PB10024) |
| Primary incubation | Overnight at 4 °C (datasheet PB10024) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet PB10024) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ACLY-positive staining in pancreatic endocrine cells of pancreas (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic and nuclear expression in several tissues. No signal in the no-primary control. |
ACLY is a cytosolic enzyme with no transmembrane segment (UniProt P53396: cytosol; topology). In paraffin-section IHC, expect predominantly cytoplasmic staining, with nuclear staining possible in several tissues (HPA: tissue IHC). Pancreatic endocrine cells, prostate glandular cells and testicular Leydig cells are reported as High (HPA: tissue IHC). Interpret tissue comparisons cautiously: HPA rates IHC reliability Enhanced but reports low consistency between staining and RNA expression (HPA: reliability description).
| Clear cytoplasmic signal in pancreatic endocrine cells, prostate glandular cells or Leydig cells. | This matches the reported High-staining cell populations (HPA: tissue IHC) and ACLY's cytosolic location (UniProt P53396: subcellular location). Compare signal with adjacent tissue and the negative control under the same detection conditions (general IHC practice). |
| Predominantly membrane-confined staining, with little cytoplasmic signal, in a reported positive population. | A membrane-only pattern conflicts with cytosolic localization and the absence of a transmembrane segment (UniProt P53396: subcellular location; topology). Review morphology and controls before calling it ACLY. Nuclear signal alone is less decisive: HPA also reports nuclear tissue staining (HPA: tissue IHC). |
| Strong staining in a cell population reported as Not detected, such as esophageal squamous epithelium. | This is discordant with that HPA observation (HPA: esophagus, squamous epithelial cells, Not detected). Cross-reactivity or endogenous chromogen-producing activity are possibilities, not diagnoses (general IHC practice). Check the no-primary control and assess whether the expected positive cell population also stains. |
| Diffuse color across cells and extracellular areas, obscuring cell boundaries. | This is background rather than an interpretable cell-specific pattern (general IHC practice). Examine the no-primary control for detection-system signal, then review blocking, washes and chromogen development (general IHC practice). HPA tissue levels do not identify the cause of background (HPA: tissue IHC). |
| No visible signal in a pancreatic endocrine-cell positive control. | That result disagrees with the reported High staining in those cells (HPA: pancreas). Before scoring the study samples negative, verify that the target cell population is present and assess retrieval, primary-antibody conditions and detection performance using the same run (general IHC practice). |
| Compartment and topology (UniProt P53396: subcellular location; topology). | Cytosolic localization and no transmembrane segment favor a cytoplasmic readout (UniProt P53396). HPA additionally observes nuclear staining in several tissues (HPA: tissue IHC); do not reject every nucleus-positive section solely on compartment. |
| Choice of tissue and cell population (HPA: tissue IHC). | Pancreatic endocrine cells, prostate glandular cells and Leydig cells are reported High; kidney tubule cells and small-intestinal glandular cells are Medium (HPA: tissue IHC). Esophageal squamous cells and rectal glandular cells are reported Not detected (HPA: tissue IHC). Score the specified cells, rather than an entire organ. |
| Strength of the tissue evidence (HPA: reliability description; antibody validation). | HPA labels the tissue IHC profile Enhanced while noting low consistency between antibody staining and RNA expression (HPA: reliability description). Four listed antibodies have Enhanced IHC validation; CAB007783 is Approved (HPA: antibodies). These labels support use of the pattern as a comparator, not a guarantee for every specimen. |
| IF/ICC expectation? (HPA: subcellular ICC-IF). | HPA reports cytosol as the supported main location in ICC-IF; nucleoplasm is uncertain, and the principal piece is an approved additional location (HPA: subcellular ICC-IF). Use that information to interpret an IF image; this section supplies no IF/ICC protocol. |
| Sequence variation and modification (UniProt P53396: isoforms; modified residues). | UniProt lists three isoforms and modified residues, including phosphorylation sites (UniProt P53396). The supplied record gives no epitope or staining effect for a particular IHC antibody, so these annotations cannot explain a changed section pattern without separate evidence. |
| Situation | Likely cause | Next action |
|---|---|---|
| The positive-control section has no chromogen in pancreatic endocrine cells. | The run may have failed at retrieval, primary-antibody binding or detection; the cause is undetermined from the slide alone (general IHC practice). Pancreatic endocrine cells are reported High (HPA: pancreas). | Confirm that endocrine cells are present, then check the run controls and optimize retrieval and antibody conditions within the assay's validated range (general IHC practice). Reassess study negatives only after the positive control works. |
| Esophageal squamous cells stain as strongly as the chosen positive control. | That conflicts with the HPA Not detected observation (HPA: esophagus). Antibody cross-reactivity or endogenous detection activity may contribute (general IHC practice). | Review the no-primary control, compare staining compartments and confirm the expected positive-cell pattern in the same run (general IHC practice; HPA: tissue IHC). Treat the discordant staining as unresolved until controls clarify it. |
| A strong signal appears only along plasma membranes. | A membrane-only distribution conflicts with ACLY's cytosolic annotation and lack of a transmembrane segment (UniProt P53396: subcellular location; topology). | Check tissue morphology, the no-primary control and whether cytoplasmic signal is present in a reported High cell population (general IHC practice; HPA: tissue IHC). Avoid scoring membrane-only color as confirmed ACLY. |
| Nuclei stain while cytoplasm is weak. | Nuclear tissue staining has been observed (HPA: tissue IHC), although cytosol is ACLY's UniProt location (UniProt P53396: subcellular location). The available evidence does not make nuclear-only staining diagnostic. | Compare the cell type and compartment with HPA tissue observations, then inspect positive and no-primary controls under the same run conditions (HPA: tissue IHC; general IHC practice). Record the nuclear-only pattern separately from an expected cytoplasmic result. |
| Diffuse chromogen obscures differences between cells. | Excess nonspecific signal or detection-system activity may obscure localization (general IHC practice); HPA staining levels do not establish the cause (HPA: tissue IHC). | Inspect the no-primary control and review blocking, washing and chromogen development; repeat with settings that preserve the positive-control cell pattern (general IHC practice; HPA: tissue IHC). |
| A Medium or Not detected HPA population gives a different result in the study specimen. | HPA reports cell-specific reference observations and notes low consistency between staining and RNA expression (HPA: tissue IHC; reliability description). A discrepant specimen alone cannot identify a technical or biological cause. | Verify the cell identity and run controls, document the compartment and intensity, and interpret the discrepancy against the relevant HPA cell-level observation (general IHC practice; HPA: tissue IHC). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Low 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 |
|---|---|---|---|---|
| Pancreas | Pancreatic endocrine cells | High | Protein (IHC) | HPA → |
| Prostate | Glandular cells | High | Protein (IHC) | HPA → |
| Testis | Leydig cells | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Cerebellum | Cells in molecular layer | Medium | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Esophagus | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
| Fallopian tube | Ciliated cells (cell body) | Not detected | Protein (IHC) | HPA → |
| Oral mucosa | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
| Ovary | Ovarian stroma cells | Not detected | Protein (IHC) | HPA → |
| Parathyroid gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot ACLY staining in paraffin sections by checking retrieval, compartment, cell type and controls before comparing signal intensity (UniProt P53396; HPA tissue IHC).
Anti-ACLY antibodies have IHC images from human tissues and mouse and rat pancreas, plus IF/ICC images from MCF7 and A594 cells (catalog image captions: M02372-1, PB10024).
PB10024 shows paraffin-section IHC in human colonic adenocarcinoma, hepatocellular carcinoma, laryngeal squamous cell carcinoma and placenta, plus IF in A594 cells (catalog image captions: PB10024); M02372-1 shows paraffin-section IHC in human pancreatic and testis cancer and mouse and rat pancreas, plus IF in MCF7 cells (catalog image captions: M02372-1). M02372 shows paraffin-section IHC in human brain carcinoma (catalog image caption: M02372); M02372-3 shows IHC staining of human hepatocellular carcinoma, with section processing unreported (catalog image caption: M02372-3).
Which to pick: For paraffin-section IHC, consider PB10024, a rabbit antibody listed at 1–2 μg/ml, or M02372-1, a mouse monoclonal listed at 0.5–1 μg/ml; each antibody’s own IHC caption documents EDTA pH 8 retrieval and DAB detection, but neither reports the fixative (catalog host/dilutions and IHC image captions: PB10024, M02372-1). For IF/ICC, M02372-1 has an MCF7 cell image and a listed dilution of 2 μg/ml, while PB10024 has an A594 cell image and a listed dilution of 5 μg/ml (catalog IF image captions/dilutions: M02372-1, PB10024). For cross-species tissue IHC, prioritize M02372-1: its own IHC captions show human, mouse and rat samples, matching its listed reactivity (catalog IHC image captions/reactivity: M02372-1).