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NR1H3 / Oxysterols receptor LXR-alpha · IHC design guide
Design Immunohistochemistry for NR1H3
Plan NR1H3 chromogenic IHC around the reported general nuclear tissue pattern (HPA tissue IHC). This guide covers fixation consistency, nuclear scoring, and interpretation given the low consistency between antibody staining and RNA expression (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
NR1H3 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Nuclear tissue staining (HPA tissue IHC) | |
| Staining pattern | Nuclear staining in glandular and hematopoietic cells (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A03331) | |
| Caveat | Antibody staining and RNA expression show low consistency (HPA tissue IHC) | |
| Regulation | Liver-enhanced RNA expression (HPA tissue RNA) | |
| Isoform / epitope | 3 isoforms; epitope coverage is unreported (UniProt) |
Section 1
Recommended NR1H3 IHC & IF Protocols
The catalog antibody's IHC-P protocol is accompanied by two published NR1H3 protocols for paraffin sections (PMC13400882; PMC6343513).
| Sample | Tissue sections; selected-image fixative not specified (standard IHC workflow) |
| Fixation | Image fixative and duration unreported (datasheet A03331); 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 Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear 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-NR1H3, 5 μg/mL (datasheet A03331) |
| 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 | NR1H3-positive staining in glandular cells of adrenal gland (HPA tissue IHC: Medium). HPA tissue profile: General nuclear expression. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA pH 9.0 at 95–98 °C for 20 min (page retrieval rule: nuclear antigen); microwave retrieval is also reported (PMC6343513).
Section 2
What Is the Expected NR1H3 Staining Pattern?
NR1H3 should appear mainly in nuclei, with possible cytoplasmic staining (UniProt Q13133: nucleus and cytoplasm; HPA: general nuclear expression). HPA reports medium IHC staining in adrenal glandular cells and bone marrow hematopoietic cells, among other listed cells (HPA tissue IHC). It has no transmembrane segment, so a membrane-only pattern is unexpected (UniProt Q13133 topology). Interpret tissue staining cautiously: HPA rates its IHC Approved but reports low consistency with RNA expression (HPA tissue IHC).
| Nuclear staining in adrenal glandular cells or bone marrow hematopoietic cells. | This matches cells with medium staining in the HPA tissue images and the reported general nuclear pattern (HPA tissue IHC). Compare stained nuclei with neighboring cells and the counterstain; intensity alone does not establish specificity, given the reported low agreement between IHC staining and RNA expression (HPA tissue IHC; standard IHC practice). |
| Strong membrane-only or extracellular staining, with little nuclear signal. | That distribution conflicts with the reported nuclear and cytoplasmic localization and lack of a transmembrane segment (UniProt Q13133; HPA tissue IHC). Check the matched negative control and tissue morphology before treating the signal as NR1H3; an unexpected compartment raises concern for background or off-target binding but does not identify its cause (standard IHC practice). |
| Prominent staining in a cell population outside the pattern being assessed. | First confirm cell identity on the counterstained section; neighboring cells can be mistaken for the intended population (standard IHC practice). If the signal remains inconsistent with the HPA cell-specific observations, compare antibody-omission and detection-only controls for nonspecific binding or endogenous detection activity (HPA tissue IHC; standard IHC practice). HPA lists low staining in liver cholangiocytes, not a universal negative result (HPA tissue IHC). |
| Diffuse brown signal across cells, stroma, or slide background. | A diffuse pattern is difficult to reconcile with predominantly nuclear NR1H3 staining (HPA tissue IHC). Review background in the negative controls and assess blocking, washes, and endogenous chromogen-generating activity as general chromogenic IHC checks (standard IHC practice). Background alone cannot establish whether target protein is present (standard IHC practice). |
| No convincing nuclear signal in an HPA medium-staining cell population. | A missing signal in, for example, adrenal glandular cells warrants checking section quality, retrieval, antibody and detection steps, and an appropriate positive control (HPA tissue IHC; standard IHC practice). It does not by itself prove absence of NR1H3: HPA reports low agreement between antibody staining and RNA expression, and its listed levels describe observations rather than guaranteed results (HPA tissue IHC). |
💡Expected NR1H3 appearanceA credible positive is chiefly nuclear staining in an HPA medium-staining cell population, such as adrenal glandular cells, with intensity judged against controls; dominant membrane-only or diffuse acellular color is suspect (HPA tissue IHC; UniProt Q13133 topology; standard IHC practice).
| Choice of tissue and cell population | HPA reports medium staining in adrenal glandular, appendix glandular, bone marrow hematopoietic, bronchial respiratory epithelial, and selected glial cells, but low staining in liver cholangiocytes (HPA tissue IHC). UniProt reports strong expression in liver, kidney, and intestine at the tissue level; that statement does not specify which cells in a section will stain (UniProt Q13133). |
| IHC evidence strength | HPA calls the tissue IHC profile Approved while explicitly noting low consistency between staining and RNA expression; both statements should accompany interpretation (HPA tissue IHC). The listed antibodies HPA036443 and CAB037109 are IHC Approved, not IHC Enhanced in the supplied record (HPA antibodies). |
| Compartment and topology | Nucleus and cytoplasm are reported locations; HPA describes general nuclear IHC expression (UniProt Q13133; HPA tissue IHC). No transmembrane segment, signal peptide, propeptide, or reported glycosylation site supports an expected membrane or secreted pattern (UniProt Q13133). These annotations do not predict antigen-retrieval conditions or fixation sensitivity (UniProt Q13133). |
| Isoforms and epitope coverage | UniProt lists three NR1H3 isoforms and a ligand-binding domain at residues 209–447 (UniProt Q13133). Interpret any isoform claim only if the chosen antibody's documented epitope supports it; the supplied HPA antibody list gives no epitope positions (HPA antibodies). |
| IF/ICC: what should the signal look like? | In the separate IF/ICC assessment, HPA reports approved nucleoplasmic localization with additional cytosolic localization and images from HeLa, U-251MG, and U2OS cells (HPA subcellular). These observations support a compartment cross-check; they do not supply an IHC-P staining protocol or establish tissue-specific intensity (HPA subcellular). |
| Situation | Likely cause | Next action |
|---|---|---|
| The positive-control section is blank. | The run may have lost usable signal during retrieval, primary-antibody incubation, or chromogenic detection (standard IHC practice). | Check the control section and each run step, then compare with a documented HPA medium-staining cell population; HPA's observations are guides, not guaranteed positivity (HPA tissue IHC; standard IHC practice). |
| The section stains brown even when primary antibody is omitted. | Detection-system background or endogenous chromogen-generating activity may be contributing (standard IHC practice). | Compare detection-only and reagent controls, review endogenous-activity blocking and washes, and interpret nuclear staining only after the control background is understood (standard IHC practice). |
| Most structures show weak, diffuse color. | Nonspecific reagent binding, inadequate washing, or detection background can obscure cell boundaries (standard IHC practice). | Review blocking, washes, antibody concentration, and detection exposure with matched controls; seek a nuclear pattern in the intended cells (HPA tissue IHC; standard IHC practice). |
| Signal appears mainly at cell borders. | A border-dominant pattern conflicts with reported localization and topology; its specific cause remains unresolved (UniProt Q13133; HPA tissue IHC). | Check morphology and negative controls, then reassess antibody specificity before scoring border staining as NR1H3 (standard IHC practice). |
| Liver cholangiocytes stain weakly despite strong liver expression in UniProt. | The sources describe different resolutions: UniProt reports tissue-level expression, while HPA lists low IHC staining specifically in cholangiocytes (UniProt Q13133; HPA tissue IHC). | Record the scored cell population and its controls; avoid assigning the tissue-level statement to cholangiocytes or calling the section a failed run on that basis alone (UniProt Q13133; HPA tissue IHC). |
| Two candidate antibodies give different cell patterns. | HPA marks both listed antibodies IHC Approved and reports low staining–RNA agreement; the supplied record does not explain a discrepancy between reagents (HPA antibodies; HPA tissue IHC). | Compare each reagent's matched controls and nuclear distribution in the same cell populations; report unresolved discordance instead of assigning specificity from intensity alone (HPA tissue IHC; standard IHC practice). |
Experiment evidence
IHC & IF images showing NR1H3 staining
A03331 · IHCImmunohistochemistry of LXR-A in rat liver tissue with LXR-A antibody at 5 μg/mL.
A03331 · IFImmunofluorescence of LXR-A in rat liver tissue with LXR-A antibody at 20 μg/mL.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000025434-NR1H3/tissue/cerebral+cortex#imid_11475959
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000025434-NR1H3/tissue/colon#imid_11475157
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000025434-NR1H3/tissue/liver#imid_11475158
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000025434-NR1H3/tissue/kidney#imid_11475167
HPA · ICC-IF HeLaHuman Protein Atlas immunofluorescence, HeLa, antibody HPA036443; green = NR1H3, blue = nucleus, red = microtubules.
HPA · ICC-IF HeLaHuman Protein Atlas immunofluorescence, HeLa, antibody HPA036443; green = NR1H3, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for NR1H3 IHC & IF
🧪Run adrenal gland first: its glandular cells should show NR1H3 staining (HPA: Medium in adrenal gland glandular cells); cells without specific staining on the same section can serve as background comparators, but should not be assumed biologically negative. HPA detects NR1H3 in all 45 scored tissues (HPA: no negative tissue rows), so use no-primary and isotype controls instead of a negative tissue.
Positive control tissue: Adrenal gland (Glandular cells, HPA Medium)
Negative control tissue: None in HPA: NR1H3 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show NR1H3 in HeLa, U-251MG, U2OS, with annotated localisation: Nucleoplasm (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and an isotype control matched to the primary antibody’s host species, immunoglobulin class and monoclonal or polyclonal format; use NR1H3 knockout material as a biological negative where available. For chromogenic staining of the adrenal section, quench endogenous peroxidase and check background on the no-primary slide (standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported; the selected A03331 rat-liver IHC caption gives 5 µg/mL but does not report a fixative (selected A03331 tissue-IHC caption). Antigen-retrieval dependency in paraffin sections is unreported, so establish retrieval conditions using the controls. ICC-IF images support detectable nucleoplasmic and cytosolic NR1H3 staining (HPA: approved subcellular locations), but the supplied evidence does not establish that IF or frozen sections are easier than paraffin IHC; assess adrenal chromogenic background with the controls.
HPA tissue IHC evidence for NR1H3
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — 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.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: NR1H3 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced NR1H3 IHC Tips
Troubleshoot NR1H3 staining in paraffin sections by checking retrieval, nuclear localisation, antibody specificity and cell level scoring.
What retrieval conditions should I try when NR1H3 nuclear staining is weak?
Start with Tris-EDTA at pH 9.0, heated to 95–98 °C for 20 min (page retrieval setting). Let sections cool in the retrieval buffer, then compare nuclear staining with an otherwise identical section processed without primary antibody (standard IHC practice). NR1H3 is mainly nuclear, with additional cytoplasmic localisation, so assess recovery in nuclei before judging diffuse cytoplasmic colour as a gain in sensitivity (UniProt Q13133 localisation; HPA subcellular). If staining remains weak, test a shorter heating time or citrate at pH 6.0 as separately labelled fallback conditions, keeping detection and exposure to chromogen constant (standard IHC optimisation).
How should I troubleshoot fixation when NR1H3 staining varies between paraffin blocks?
NR1H3 specific sensitivity to fixation is unknown from the supplied evidence; the rat liver IHC caption reports 5 µg/mL antibody but does not state a fixative (A03331 tissue IHC caption). Record the fixative, fixation duration, tissue thickness and processing history for each block before changing retrieval or antibody concentration (standard IHC practice). Compare sections from blocks with matched processing and include a consistently stained reference section in each run to distinguish block variation from run variation (standard IHC practice). Avoid attributing weak staining to a particular fixation chemistry solely from the nuclear localisation or absence of a transmembrane segment (UniProt Q13133 localisation and topology).
How do I assess nuclear versus cytoplasmic NR1H3 staining?
Score nuclear and cytoplasmic staining separately because NR1H3 is reported in both compartments (UniProt Q13133 localisation). Nucleoplasm is the approved main location, while cytosol is an additional approved location, making nuclear signal the clearest compartmental reference for this assay (HPA subcellular). Check intact cell borders and a clear nuclear counterstain before calling brown colour cytoplasmic; compare each compartment with the no primary control on the same tissue type (standard IHC practice). If signal obscures nuclei or spreads across adjacent structures, shorten chromogen development and inspect thinner, well preserved areas before assigning a biological localisation (standard IHC practice).
Can this IHC result distinguish NR1H3 isoforms or epitope masking?
NR1H3 has 3 listed isoforms and an NR ligand binding domain at residues 209–447 (UniProt Q13133 isoforms and domains). The supplied caption does not identify the A03331 immunogen or epitope, so a positive section cannot establish which isoform the antibody detects (A03331 tissue IHC caption). Request epitope information for the exact catalog antibody and compare it with isoform sequences before making an isoform specific claim (standard antibody validation practice). To probe masking in paraffin sections, change retrieval conditions one variable at a time and require the expected cellular pattern plus suitable controls, since a stronger chromogen signal alone cannot establish specificity (standard IHC practice).
How should I follow up chromogenic NR1H3 findings with multiplex IF?
On the separate IF/ICC workflow, pair NR1H3 with a validated marker for the cell population being examined, and use a nuclear stain to assign signals to individual cells (standard multiplex IF practice). NR1H3 is mainly nucleoplasmic with additional cytosolic localisation, so permeabilise sufficiently to expose intracellular epitopes while checking that cell boundaries remain interpretable (HPA subcellular; standard IF practice). Choose fluorophores after inspecting unstained tissue for autofluorescence, favouring channels with the clearest separation from that background (standard IF practice). Include single colour and no primary controls to assess spectral bleed through and nonspecific fluorescence; assess IF fixation separately because the supplied rat liver IHC caption gives no fixation conditions (standard IF practice; A03331 tissue IHC caption).
What should I check when DAB background hides NR1H3 staining?
First compare the stained section with a no primary control to separate primary antibody dependent staining from detection or tissue background (standard IHC practice). In peroxidase based chromogenic IHC, block endogenous peroxidase and check whether shortening DAB development reveals distinct nuclei without excessive diffuse colour (standard IHC practice). Titrate the primary antibody around a documented starting point only in the matching context: 5 µg/mL is reported for A03331 staining of rat liver, with fixative unreported (A03331 tissue IHC caption). Also inspect folds, section edges and damaged regions independently, since local staining there can distort judgments about NR1H3 localisation (standard IHC practice).
How should I quantify NR1H3 staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, then report the percentage of positive nuclei and nuclear intensity or an H-score using consistent thresholds (standard IHC quantification practice; HPA subcellular). Count evaluable cells within matched tissue regions and normalise positive counts to total cells assessed, or report positive cell density per mm² when sampling areas differ (standard IHC quantification practice). Record cytoplasmic staining separately because NR1H3 also has a reported cytosolic location (HPA subcellular). Keep retrieval, imaging and chromogen development consistent across sections, and exclude necrotic or folded areas using prespecified rules so technical variation does not drive group differences (standard IHC practice).
When is an apparent NR1H3 positive cell likely to be an artefact?
A convincing NR1H3 result should show interpretable cellular staining, especially in nuclei, consistent with its approved main nucleoplasmic location (HPA subcellular). Consider cell identity: UniProt reports stronger expression in liver, kidney and intestine, while HPA reports low staining in liver cholangiocytes, so a cell type claim needs direct morphological assessment (UniProt Q13133 tissue specificity; HPA tissue IHC). Treat staining confined to section edges, necrotic areas or the no primary control as suspect, and check endogenous peroxidase when DAB remains brown without primary antibody (standard IHC practice). Interpret intensity cautiously because HPA labels its tissue IHC reliability Approved while reporting low consistency between antibody staining and RNA expression (HPA tissue IHC).
Boster reagents
Best NR1H3 / Oxysterols receptor LXR-alpha IHC Antibodies
A03331 has rat liver IHC and IF images (catalog image captions); its listed reactivity covers human, mouse and rat (catalog: reactivity).
Real IHC data
Anti-LXR-A NR1H3 Antibody
Cat # A03331
A03331 is the SKU with an IHC card, showing rat liver tissue stained at 5 μg/mL (A03331 IHC image caption). The catalog also shows rat liver IF at 20 μg/mL for A03331 (A03331 IF image caption).
Which to pick: Choose A03331 for paraffin-section IHC (catalog: IHC-P); its own IHC image shows rat liver at 5 μg/mL, and the fixative is unreported (A03331 IHC image caption). For IF/ICC, M03331 is a rabbit monoclonal with both applications listed, while A03331 has a rat liver IF image (catalog: M03331 host, clone and applications; A03331 IF image caption). Both list human, mouse and rat reactivity for cross-species planning (catalog: reactivity); the supplied images demonstrate rat liver only (A03331 IHC and IF image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q13133 (NR1H3_HUMAN, Oxysterols receptor LXR-alpha).
- Human Protein Atlas. NR1H3 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. NR1H3 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the cytosol..
- Human Protein Atlas. NR1H3 antibody validation summary (2 antibodies).
- Development and Validation of a Novel PPAR Signaling Pathway-Related Predictive Model to Predict Prognosis in Breast Cancer. Journal of immunology research 2022 — PMC9184151.
- Multiplex immunohistochemistry defines two cholesterol metabolism patterns predicting immunotherapeutic outcomes in gastric cancer. Journal of translational medicine 2023 — PMC10702056.
- Lappaconitine hydrobromide prevents NLRP3-GSDMD-mediated pyroptosis to alleviate sepsis-induced acute lung injury by enhancing NR1H3. Journal of pharmaceutical analysis 2026 — PMC13400882.
- Expression of NR1H3 in endometrial carcinoma and its effect on the proliferation of Ishikawa cells in vitro. OncoTargets and therapy 2019 — PMC6343513.
- PubMed PMID:7744246 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:16554811 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for NR1H3 (Oxysterols receptor LXR-alpha). Expected localisation Nuclear tissue staining (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: A03331 at 5 μg/mL (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative None in HPA (detected in all 45 tissues); use no-primary + isotype controls. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Tissue sections; selected-image fixative not specified (standard IHC workflow); 2. Fixation: Image fixative and duration unreported (datasheet A03331); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-NR1H3, 5 μg/mL (datasheet A03331); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A03331); Caveat: Antibody staining and RNA expression show low consistency (HPA tissue IHC); Isoform / epitope: 3 isoforms; epitope coverage is unreported (UniProt); Regulation: Liver-enhanced RNA expression (HPA tissue RNA). Evidence: UniProt Q13133, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet A03331, PMC13400882, PMC6343513. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/NR1H3/immunohistochemistry-ihc-guide.