NLRP3 / NACHT, LRR and PYD domains-containing protein 3 · IHC design guide

Design Immunohistochemistry for NLRP3

Plan chromogenic IHC on paraffin sections around the cytoplasmic tissue pattern reported for NLRP3 (HPA tissue IHC). Use the staining controls and scoring guidance to interpret a tissue profile whose reliability is uncertain (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for NLRP3 (IHC for NLRP3): expected localisation Cytoplasmic tissue staining; organelle association is a molecular expectation (HPA tissue IHC; UniProt), antibody M00034, validated IHC image, and IHC protocol steps
Printable NLRP3 IHC protocol sheet — expected localisation Cytoplasmic tissue staining; organelle association is a molecular expectation (HPA tissue IHC; UniProt), antibody M00034, controls and protocol steps. Open the full NLRP3 IHC guide →

NLRP3 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 Cytoplasmic tissue staining; organelle association is a molecular expectation (HPA tissue IHC; UniProt)
Staining pattern Cytoplasmic staining in several tissues, including bone marrow (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 ⓘ Adipose tissue+4 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep tissue fixation consistent (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image M00034)
Caveat Tissue staining has low consistency with RNA expression (HPA tissue IHC)
Regulation LPS-treated granulocytes express NLRP3 (UniProt)
Isoform / epitope Six isoforms; verify that the antibody epitope is shared (UniProt)
Section 1

Recommended NLRP3 IHC & IF Protocols

The catalog antibody’s IHC-P protocol is accompanied by three published NLRP3 IHC protocols for ovary, intestinal tissue, and liver sections (PMC6842944; PMC12720632; PMC5331985).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human lung carcinoma tissue; fixative not specified (datasheet M00034)
FixationImage fixative and duration unreported (datasheet M00034); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibodyRabbit monoclonal (clone FBD-14) anti-NLRP3, 1:50-1:200 (datasheet M00034)
Primary incubationOvernight at 4 °C (standard)
DetectionHRP-polymer secondary, DAB chromogen 5–10 min (standard)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultNLRP3-positive staining in glandular cells of adrenal gland (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression in several tissues including bone marrow. No signal in the no-primary control.
💡Decision noteStart with Tris-EDTA pH 9.0 HIER at 95–98 °C for 20 min (page retrieval); a liver protocol reports microwave retrieval without specifying buffer or duration (PMC5331985).
Section 2

What Is the Expected NLRP3 Staining Pattern?

NLRP3 is mainly cytosolic in resting macrophages and can associate with organelle membranes; it has no transmembrane segment (UniProt Q96P20 localization and topology). In paraffin sections, expect cytoplasmic staining in appropriate cells, including macrophages and some epithelial cells (UniProt Q96P20 tissue specificity; HPA tissue IHC). Treat tissue patterns cautiously: HPA rates the IHC evidence Uncertain because antibody staining and RNA expression have low consistency (HPA tissue IHC).

What am I looking at on my slide?
Cytoplasmic staining in cells with macrophage morphology, or in selected epithelial cells.This fits the predominant macrophage expression and mainly cytosolic resting location reported by UniProt. Epithelial staining can also fit the record: HPA reports medium staining in bronchial respiratory epithelium and cervical squamous epithelium. Identify the stained cell type before scoring; the HPA tissue pattern remains Uncertain (UniProt Q96P20 tissue specificity and localization; HPA tissue IHC).
Punctate cytoplasmic staining, or staining concentrated near a subset of intracellular structures.Organelle-associated or concentrated signal is biologically plausible: UniProt places resting NLRP3 on endoplasmic reticulum, mitochondrial and Golgi membranes, and describes redistribution during activation. A punctum alone cannot establish inflammasome activation in a chromogenic section; assess cell identity and staining controls before interpreting its significance (UniProt Q96P20 localization; general IHC interpretation).
Predominantly nuclear staining across many cells, with little cytoplasmic signal.Check for an artefact or nonspecific signal before assigning this as the general tissue pattern. UniProt describes mainly cytosolic resting macrophage NLRP3, but also reports nuclear localization in Th2 helper T cells, so nuclear staining is not categorically impossible. Interpretation depends on cell identity and context (UniProt Q96P20 localization).
Strong staining in a cell population recorded as not detected, or diffuse color across the section.Consider cross-reactivity, endogenous detection activity or background. For example, HPA records adipocytes and cardiomyocytes as Not detected; those entries are useful comparisons, not definitive exclusions, given HPA's Uncertain IHC reliability. Color outside recognizable cells also argues for a technical background check (HPA tissue IHC; general IHC practice).
No signal in a section expected to contain NLRP3-expressing cells.First confirm that the expected cells are present: UniProt reports predominant macrophage expression and very weak monocyte protein expression. A blank slide may reflect low target abundance or an IHC workflow problem; it does not by itself overturn those expression records. Compare with a processed positive tissue section and detection controls (UniProt Q96P20 tissue specificity; general IHC practice).
💡Expected NLRP3 appearanceA credible positive is cell-associated, mainly cytoplasmic staining in appropriate cells, with medium epithelial staining possible in HPA-listed sites; widespread nuclear-only color or diffuse color without cell boundaries needs scrutiny (UniProt Q96P20 localization and tissue specificity; HPA tissue IHC; general IHC interpretation).
How each factor affects the staining
Cell population and tissue contextUniProt reports predominant macrophage expression, weak monocyte protein expression and protein in selected epithelia. HPA reports medium staining in several epithelial populations, but calls its overall IHC reliability Uncertain. Score identified cell populations rather than treating every stained cell in a tissue as equivalent evidence (UniProt Q96P20 tissue specificity; HPA tissue IHC).
Resting state and activationUniProt describes resting macrophage NLRP3 as mainly cytosolic and organelle-associated; activation can redistribute it through the microtubule organizing center to dispersed trans-Golgi vesicles. The record does not establish a diagnostic chromogenic punctum pattern, so use morphology and appropriate independent evidence before calling activation from NLRP3 staining alone (UniProt Q96P20 localization and function).
Antibody validationHPA lists antibody HPA012878 as Uncertain for IHC and gives the tissue profile Uncertain reliability because staining and RNA expression have low consistency. Treat agreement with an HPA example as supportive rather than definitive; compare cell identity and controls when interpreting an unexpected positive (HPA antibodies; HPA tissue IHC).
IF/ICC Q: What pattern can this page support?A: UniProt supports mainly cytosolic resting macrophage localization and context-dependent redistribution. HPA supplies no main ICC-IF location and no cell-line ICC-IF images, so it provides no image-based IF pattern to confirm here. This IHC section does not specify an IF protocol (UniProt Q96P20 localization; HPA subcellular ICC-IF).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
The entire section has weak brown haze.Nonspecific background or endogenous detection activity can obscure cell-associated staining (general chromogenic IHC practice).Review the no-primary control, blocking and wash steps, and detection chemistry. Judge any remaining signal by recognizable cells and compartments; HPA describes a cytoplasmic tissue profile, albeit with Uncertain reliability (general IHC practice; HPA tissue IHC).
Most cells show nuclear-only staining.The distribution conflicts with the mainly cytosolic resting macrophage location, though UniProt allows nuclear NLRP3 in Th2 cells (UniProt Q96P20 localization).Identify the stained population and compare controls before calling artefact. If the pattern is broad and lacks a plausible Th2 context, review primary-antibody specificity and detection background (UniProt Q96P20 localization; general IHC practice).
An expected positive section is blank.Expected cells may be absent or scarce, or a general staining step may have failed; UniProt reports weak monocyte protein expression (UniProt Q96P20 tissue specificity; general IHC practice).Confirm cell composition, then check the positive control, antibody application, retrieval procedure and detection reagents according to the selected IHC workflow. Do not assign an NLRP3-specific retrieval requirement from these sources (general IHC practice).
Adipocytes or cardiomyocytes stain strongly.HPA records these cell types as Not detected, making strong signal unexpected, while its overall IHC reliability remains Uncertain (HPA tissue IHC).Verify cell identification and compare no-primary and independent staining controls. Investigate background or cross-reactivity before reporting NLRP3 in those cells; an HPA not-detected entry alone cannot prove absence (HPA tissue IHC; general IHC practice).
Only small puncta appear in otherwise negative cells.UniProt describes NLRP3 redistribution with activation, but puncta by themselves do not establish an active inflammasome in IHC (UniProt Q96P20 localization; general IHC interpretation).Check whether puncta are intracellular and confined to plausible cell types, then compare section controls. Reserve an activation claim for additional evidence beyond this NLRP3 pattern (UniProt Q96P20 localization; general IHC interpretation).
A medium-staining epithelial site gives variable results between sections.HPA's epithelial staining observations have Uncertain reliability, and differing cell composition can affect the observed pattern (HPA tissue IHC; general IHC interpretation).Compare the same identified epithelial population across sections and review the processed positive control. Report the observed compartment and intensity with the HPA reliability caveat, without inferring a target-specific fixation effect (HPA tissue IHC; general IHC practice).

Sample controls for NLRP3 IHC & IF

🧪Run bronchus first: respiratory epithelial cells should stain at a Medium level (HPA: bronchus, respiratory epithelial cells, Medium). Use fallopian tube glandular cells as the negative tissue (HPA: Not detected); on the bronchus slide, cells outside the stained epithelial compartment should show background-level signal, while infiltrating macrophages should not be assumed negative (UniProt Q96P20: predominantly expressed in macrophages).
Positive control tissue: Adrenal gland (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for NLRP3; derive a cell-line control from the positive tissue's cell type (Glandular cells) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary (secondary-only) slide, an isotype control matched to the primary antibody’s host species and clonality, and NLRP3-knockout material or a validated immunizing-peptide block as a biological specificity control (standard IHC practice). For bronchus, quench endogenous peroxidase and check inflammatory cells for residual background before scoring epithelial stain (standard chromogenic IHC practice).
⚠️Feasibility: A target-specific fixation window and retrieval dependency are unreported in the supplied evidence; optimize antigen retrieval with the catalog antibody before scoring (standard IHC practice). The selected paraffin-section lung carcinoma caption does not state a fixative (SKU M00034 caption: fixative unreported). The evidence does not establish that frozen sections or IF are easier; bronchial mucus and inflammatory cells warrant a background check during chromogenic interpretation (standard IHC practice).

HPA tissue IHC evidence for NLRP3

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — 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

TissueCell typeLevelEvidenceSource
Adrenal gland Glandular cells Medium Protein (IHC) HPA →
Appendix Glandular cells Medium Protein (IHC) HPA →
Bronchus Respiratory epithelial cells Medium Protein (IHC) HPA →
Cerebral cortex Neuronal cells Medium Protein (IHC) HPA →
Cervix Squamous epithelial cells Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes Not detected Protein (IHC) HPA →
Caudate Glial cells Not detected Protein (IHC) HPA →
Cerebellum Cells in granular layer Not detected Protein (IHC) HPA →
Fallopian tube Glandular cells Not detected Protein (IHC) HPA →
Heart muscle Cardiomyocytes Not detected Protein (IHC) HPA →
Section 3

Advanced NLRP3 IHC Tips

Troubleshoot NLRP3 staining in paraffin sections by checking retrieval, cell identity, signal location and controls before comparing samples.

How should I troubleshoot weak NLRP3 staining after antigen retrieval?
Use Tris-EDTA pH 9.0 heat-induced epitope retrieval at 95–98 °C for 20 min for paraffin sections (page retrieval setting: M00034). Allow sections to cool consistently, then compare staining across sections processed with the same heating and detection conditions (standard IHC practice). If signal remains weak, check tissue adhesion, primary antibody concentration and a positive control before extending retrieval time, since excessive heating can damage section morphology (standard IHC practice). Judge improvement by cellular staining: NLRP3 is mainly cytosolic in resting macrophages and can associate with organelle membranes (UniProt Q96P20 subcellular location).
Could fixation explain weak or uneven NLRP3 staining?
Target-specific sensitivity to fixation is unknown from the supplied evidence; the M00034 image identifies paraffin-embedded human lung carcinoma but does not state its fixative (M00034 tissue-IHC caption). Record the fixative, fixation duration and processing history for each specimen before attributing differences in staining to NLRP3 abundance (standard IHC practice). If comparable sections are available, process them together with the same retrieval and detection conditions, then assess both staining and preserved morphology (standard IHC practice). Do not infer a preferred fixative from reported tissue staining patterns or from NLRP3 localisation and modifications (HPA tissue IHC; UniProt Q96P20 subcellular location and modified residues).
Which NLRP3 staining patterns are plausible in tissue sections?
Assess staining within identified cells rather than treating every brown deposit as NLRP3: resting macrophages contain mainly cytosolic and organelle-associated protein (UniProt Q96P20 subcellular location). Activation can redistribute NLRP3 through the microtubule organizing center to dispersed trans-Golgi vesicle membranes, so a focal intracellular pattern can be plausible (UniProt Q96P20; PubMed:39173637). Nuclear staining requires cell-context scrutiny because nuclear localisation is described for Th2 helper T cells, whereas Th1 cells are mainly cytoplasmic (UniProt Q96P20 subcellular location). Compare intact cells at matched magnification and counterstain quality; routine chromogenic IHC alone cannot establish inflammasome assembly from a punctum (standard IHC interpretation; UniProt Q96P20 function).
How can epitope uncertainty affect NLRP3 IHC interpretation?
Confirm the catalog antibody’s stated immunogen or mapped epitope before interpreting selective staining, since the supplied M00034 caption does not identify that region (M00034 tissue-IHC caption). NLRP3 has 6 listed isoforms and includes a pyrin domain at residues 1–93, FISNA at 140–210 and NACHT at 220–536 (UniProt Q96P20 isoforms and domains). An epitope’s presence across isoforms cannot be established here without its sequence or mapped region (UniProt Q96P20 isoforms; M00034 tissue-IHC caption). If staining disagrees with expected cell distribution, compare independently mapped antibodies or an orthogonal expression measure while keeping retrieval and section handling comparable (standard IHC validation practice).
How should I assess NLRP3 by IF alongside this IHC guide?
Use the separate IF/ICC guide for method selection; the supplied M00034 tissue image documents paraffin-section IHC, not IF validation (M00034 tissue-IHC caption). For multiplex IF, pair NLRP3 with a validated macrophage marker when that cell population is under study, because macrophages are a predominant expression site (UniProt Q96P20 tissue specificity). Choose fluorophores after checking unstained tissue autofluorescence, favoring channels with a clear signal-to-background separation, and include single-stain controls for bleed-through (standard IF practice). NLRP3 lacks a transmembrane segment and is mainly intracellular, so assess permeabilisation for access to its cytosolic or organelle-associated epitope without assuming the antibody’s epitope location (UniProt Q96P20 topology and subcellular location).
What should I check when NLRP3 staining is diffusely brown?
Compare a no-primary control and an isotype control where appropriate to identify detection-system or nonspecific staining before adjusting the primary antibody (standard IHC practice). Check peroxidase blocking and DAB development time, especially when pigment or endogenous enzyme activity may resemble chromogen signal; these are general workflow checks (standard chromogenic IHC practice). Titrate the primary antibody and review blocking and washes on matched sections, judging changes against cellular morphology rather than overall darkness (standard IHC practice). NLRP3 can occupy cytosol and organelle membranes, but a uniform extracellular haze is not established as its resting cellular distribution (UniProt Q96P20 subcellular location).
How can I quantify NLRP3 IHC across samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the tissue region and cell population before scoring, then report the percentage of positive cells and staining intensity or an H-score from 0–300 (standard IHC scoring practice). If counting discrete positive cells, report density per mm² of viable tissue and exclude folds, edges and necrotic regions by a prespecified rule (standard IHC quantification practice). Normalise within the same cell population or area definition, and keep section processing, retrieval, chromogen development and image thresholds consistent across samples (standard IHC quantification practice). Record macrophage-rich regions separately when relevant, because NLRP3 expression is predominantly reported in macrophages (UniProt Q96P20 tissue specificity).
How do I distinguish true NLRP3 staining from artefact?
A convincing result is reproducible cellular staining in a biologically plausible population, interpreted with a negative detection control and tissue morphology (standard IHC interpretation; UniProt Q96P20 tissue specificity). Scrutinise nuclear-only staining outside a defined Th2 context, because resting macrophage NLRP3 is mainly cytosolic or organelle-associated (UniProt Q96P20 subcellular location). Exclude edge staining, necrotic deposits and residual endogenous peroxidase signal before calling focal brown material positive (standard chromogenic IHC practice). Treat an isolated punctum cautiously: NLRP3 can participate in an inflammasome, but chromogenic appearance alone does not demonstrate activation, and HPA rates its tissue-IHC pattern uncertain because antibody staining has low consistency with RNA data (UniProt Q96P20 function; HPA tissue IHC reliability).
Boster reagents

Best NLRP3 / NACHT, LRR and PYD domains-containing protein 3 IHC Antibodies

Anti-NLRP3 antibodies have IHC images from paraffin-embedded human lung carcinoma and rat kidney tissue, plus IF data from Raw264.7 cells (catalog image captions). Listed reactivity covers human, mouse, and rat (catalog reactivity).

Real IHC data Immunohistochemical analysis of paraffin-embedded human lung carcinoma, using NALP3 Antibody.
Anti-NALP3 NLRP3 Rabbit Monoclonal Antibody
Cat # M00034
Real IHC data Rat kidney tissue was stained with Anti-NLRP3 rabbit Antibody
Anti-NLRP3 Rabbit Monoclonal Antibody
Cat # M00034-1

M00034 lists IHC and IF/ICC, with images of paraffin-embedded human lung carcinoma by IHC and Raw264.7 cells by IF (catalog applications and image captions). M00034-1 lists IHC and IF, with an IHC image of rat kidney tissue (catalog applications and image caption).

Which to pick: Choose M00034 for human paraffin-section IHC or IF/ICC: it is a human-reactive rabbit monoclonal with those listed applications and corresponding images (catalog reactivity, applications and image captions). Choose M00034-1 for work spanning human, mouse, or rat: it is a rabbit monoclonal listed for IHC and IF, with an IHC image from rat kidney tissue (catalog reactivity, applications and image caption). The M00034 caption specifies paraffin embedding but no fixative; the M00034-1 caption reports neither processing method nor fixative (catalog IHC image captions).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q96P20 (NLRP3_HUMAN, NACHT, LRR and PYD domains-containing protein 3).
  2. Human Protein Atlas. NLRP3 tissue IHC expression (reliability: Uncertain).
  3. Human Protein Atlas. NLRP3 subcellular location (ICC-IF): Highest expression in THP-1: 68.3 nTPM.
  4. Human Protein Atlas. NLRP3 antibody validation summary (1 antibodies).
  5. Expression and Contribution of NLRP3 Inflammasome During the Follicular Development Induced by PMSG. Frontiers in cell and developmental biology 2019 — PMC6842944.
  6. NLRP3 Inflammasome Plays an Important Role in the Pathogenesis of Collagen-Induced Arthritis. Mediators of inflammation 2016 — PMC4807043.
  7. Kaempferol activity on Cryptosporidium parvum infection in an experimentally infected immunocompromised mouse model: In silico and in vivo investigations. Pharmaceutical biology 2026 — PMC12720632.
  8. Microvesicles released from fat-laden cells promote activation of hepatocellular NLRP3 inflammasome: A pro-inflammatory link between lipotoxicity and non-alcoholic steatohepatitis. PloS one 2017 — PMC5331985.
  9. PubMed PMID:11687797 — UniProt-cited evidence.
  10. PubMed PMID:12355493 — UniProt-cited evidence.
  11. PubMed PMID:11786556 — UniProt-cited evidence.