This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
BNIP3L / BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like · IHC design guide
Design Immunohistochemistry for BNIP3L
Plan BNIP3L chromogenic IHC in paraffin sections with the IHC-validated antibody at 1:50 (datasheet M03107). Assess cytoplasmic staining, which is often granular, using kidney tubules as a high-staining reference (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
BNIP3L 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 | Observed cytoplasm (HPA tissue IHC); mitochondrial outer membrane (UniProt) | |
| Staining pattern | Broad cytoplasmic staining, often granular (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M03107) | |
| Positive control | Breast+4 more · see all | |
| Negative control | Soft tissue |
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 M03107) | |
| Caveat | Chondrocytes show no detectable staining (HPA tissue IHC) | |
| Regulation | PPTC7 interaction promotes degradation (UniProt) | |
| Isoform / epitope | Two isoforms; antibody epitope coverage is unspecified (UniProt) |
Section 1
Recommended BNIP3L IHC & IF Protocols
The catalog antibody has an IHC-P protocol (datasheet M03107). Three published BNIP3L IHC examples provide tissue-specific starting points (PMC8258758; PMC2360231; PMC11872638).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet M03107) |
| Fixation | Image fixative and duration unreported (datasheet M03107); 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 M03107); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M03107) |
| Primary antibody | Rabbit monoclonal (clone ABIB-2) anti-BNIP3L, 1:50 (datasheet M03107) |
| Primary incubation | Overnight at 4 °C (datasheet M03107) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M03107) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | BNIP3L-positive staining in myoepithelial cells of breast (HPA tissue IHC: High). HPA tissue profile: Ubiquitous cytoplasmic expression, which often had a granular pattern. No signal in the no-primary control. |
💡Decision noteFor the catalog antibody, start with heat-mediated EDTA retrieval at pH 8.0 (datasheet M03107). The published protocols used different retrieval conditions where specified (PMC2360231; PMC11872638).
Section 2
What Is the Expected BNIP3L Staining Pattern?
In paraffin-section IHC, expect mainly cytoplasmic, often granular BNIP3L staining (HPA: tissue IHC profile), consistent with an outer mitochondrial membrane protein whose transmembrane segment spans residues 188–208 (UniProt O60238: localization and topology). Staining is widespread, with high signal reported in selected glandular, epithelial and other cell populations (HPA: tissue IHC). HPA rates the tissue pattern Enhanced, while reporting medium consistency with RNA expression (HPA: reliability description).
| Granular cytoplasmic staining in kidney tubular cells, with a clear cellular pattern. | This fits the expected compartment and a reported high-staining population (HPA: ubiquitous, often granular cytoplasmic pattern; High in kidney tubular cells). Judge signal against neighboring tissue and controls, since HPA's Enhanced rating still carries medium RNA–staining consistency (HPA: reliability description). |
| Staining is confined to nuclei, cell surfaces or extracellular material, with little cytoplasmic signal. | This departs from the tissue IHC pattern (HPA: cytoplasmic, often granular). Treat it as suspect and check controls; a nuclear-envelope location is annotated (UniProt O60238: localization), and nuclear speckles are an additional ICC-IF location (HPA: subcellular), so nuclear signal alone cannot prove an artefact. |
| The strongest color appears in cells expected to stain little, while a known high-staining population is faint. | Consider nonspecific binding or endogenous detection activity before assigning that contrast to BNIP3L (general IHC practice). HPA reports low staining in adipocytes and cholangiocytes, and high staining in kidney tubular cells and endometrial glandular cells; these are comparative references, not absolute sample-level thresholds (HPA: tissue IHC). |
| A uniform brown haze covers cells and extracellular spaces, obscuring granular detail. | Diffuse background prevents a reliable localization call (general IHC practice). Review the negative reagent control and detection background, then compare with the reported cytoplasmic pattern (HPA: tissue IHC); overall color intensity by itself does not establish specific BNIP3L staining (general IHC practice). |
| No signal appears in a section containing a reported high-staining cell population. | Check whether that cell population is present and intact before calling the stain negative (general IHC practice). HPA reports high staining in, for example, breast myoepithelial cells and lung type II alveolar cells (HPA: tissue IHC); the reported level does not guarantee positivity in every specimen. |
💡Expected BNIP3L appearanceCall a positive result when identifiable cells show cytoplasmic, often granular signal, especially in a reported high-staining population (HPA: tissue IHC); broad extracellular color or a slide-wide haze is a false-positive warning sign (general IHC practice).
| Compartment and topology | BNIP3L is annotated at the mitochondrial outer membrane, endoplasmic reticulum and nuclear envelope, with one transmembrane segment at residues 188–208 (UniProt O60238: localization and topology). HPA's paraffin-section observation is cytoplasmic, often granular staining (HPA: tissue IHC); an IHC image need not resolve individual mitochondria (general IHC practice). |
| Tissue and cell selection | HPA describes widespread cytoplasmic expression but different cell-level intensities: High in prostate glandular cells and ovarian follicle cells, Low in adipocytes, and Not detected in soft-tissue chondrocytes (HPA: tissue IHC). Score the identified cell population, not the whole section as one uniform positive or negative field (general IHC practice). |
| Strength of the reference pattern | Two listed antibodies have Enhanced IHC validation, while HPA reports medium consistency between antibody staining and RNA expression (HPA: antibody validation and reliability description). This supports using the pattern as a reference, with controls and morphology when interpreting discordant cells (general IHC practice). |
| IF/ICC: what location is expected? | HPA reports mitochondria as the main ICC-IF location, with nuclear speckles as an additional location (HPA: subcellular). Use that as an IF/ICC interpretation reference; the paraffin-section IHC pattern remains cytoplasmic and often granular (HPA: tissue IHC). |
| Isoforms and specimen processing | UniProt lists two isoforms and no signal peptide or propeptide (UniProt O60238: isoforms and processing). The supplied records do not identify an antibody epitope or establish isoform-dependent IHC staining or BNIP3L-specific fixation sensitivity; do not infer those effects from the topology or HPA tissue levels. |
| Situation | Likely cause | Next action |
|---|---|---|
| A reported high-staining population is blank. | The expected cells may be absent from the section, or the staining run may have failed (HPA: cell-specific tissue levels; general IHC practice). | Confirm cell identity on morphology, check a concurrent positive control, then review the catalog antibody's IHC-P instructions for retrieval, dilution and detection (general IHC practice). Do not assign a BNIP3L-specific retrieval or fixation effect without evidence. |
| The entire section has diffuse chromogen. | Background from detection chemistry, insufficient blocking or excessive primary antibody is possible (general IHC practice). | Inspect a negative reagent control; check blocking, washes, primary concentration and detection conditions (general IHC practice). Seek discrete cytoplasmic detail before scoring against the HPA pattern (HPA: tissue IHC). |
| Strong staining appears mainly in a low-staining reference population. | Nonspecific binding or endogenous detection activity is possible, although HPA cell-level intensities are references rather than guarantees (HPA: tissue IHC; general IHC practice). | Compare the suspect cells with a reported high-staining population and negative reagent control; inspect whether the signal is granular and cytoplasmic (HPA: tissue IHC; general IHC practice). |
| Only nuclear staining is visible. | The result differs from HPA's tissue IHC pattern; nuclear-envelope localization is annotated, so compartment alone cannot establish its cause (HPA: tissue IHC; UniProt O60238: localization). | Check the negative reagent control and repeat interpretation against cytoplasmic signal in a reported high-staining population (HPA: tissue IHC; general IHC practice). Treat nuclear-only IHC as unresolved pending independent confirmation. |
| Soft-tissue chondrocytes show clear staining. | HPA reports BNIP3L as Not detected in that cell population; nonspecific signal is one possibility (HPA: tissue IHC; general IHC practice). | Verify that the stained cells are chondrocytes, inspect background controls and compare the pattern with a reported high-staining cell population (HPA: tissue IHC; general IHC practice). Avoid treating all soft tissue as an equivalent negative control. |
| A positive-looking field cannot be scored confidently. | Mixed cell populations or diffuse background may hide which cells carry the signal (general IHC practice). | Identify cells with the counterstain and tissue morphology, then score localization and intensity by cell population (general IHC practice). Use HPA's named high, low and undetected populations as references, while retaining its medium RNA–staining consistency caveat (HPA: tissue IHC and reliability description). |
Experiment evidence
IHC & IF images showing BNIP3L staining
M03107 · IHCIHC analysis of BNIP3L using anti-BNIP3L antibody (M03107). BNIP3L was detected in a paraffin-embedded section of human liver cancer tissue.
M03107 · IHCIHC analysis of BNIP3L using anti-BNIP3L antibody (M03107). BNIP3L was detected in a paraffin-embedded section of human rectal cancer tissue
A03107 · IHCImmunohistochemical staining of human kidney tissue using Bnip3L antibody at 2 μg/mL.
A03107 · IFImmunofluorescence of Bnip3L in Human Kidney tissue with Bnip3L antibody at 10 μg/mL.
A03107-3 · IFIF analysis of BNIP3L using anti-BNIP3L antibody (A03107-3). BNIP3L was detected in an immunocytochemical section of U2OS cells. Enzyme anti
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000104765-BNIP3L/tissue/cerebral+cortex#imid_6427584
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000104765-BNIP3L/tissue/colon#imid_6424350
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000104765-BNIP3L/tissue/liver#imid_6424359
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000104765-BNIP3L/tissue/kidney#imid_6424344
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA015652; green = BNIP3L, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA015652; green = BNIP3L, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for BNIP3L IHC & IF
🧪Run kidney first: cells in tubules should stain (HPA: High in kidney cells in tubules). Use soft tissue chondrocytes as the negative tissue (HPA: Not detected in chondrocytes); on the kidney slide, treat any unstained cells outside tubules as internal background references, without assuming they are BNIP3L-negative.
Positive control tissue: Breast (Myoepithelial cells, HPA High)
Negative control tissue: Soft tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show BNIP3L in A-431, U-251MG, U2OS, with annotated localisation: Mitochondria (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and a rabbit IgG isotype control matched to the primary antibody (caption: rabbit anti-BNIP3L and anti-rabbit secondary); use BNIP3L knockout material, if available, as a biological specificity control. Quench endogenous peroxidase and inspect the no-primary kidney section for DAB background (caption: HRP/DAB detection).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected M03107 paraffin-section caption does not state the fixative (caption: fixative not stated). The reported IHC conditions use heat retrieval in EDTA at pH 8.0, followed by primary antibody at 1:50 overnight at 4°C (caption: M03107 tissue IHC); retrieval dependence has not been established. The evidence does not establish that frozen sections or IF are easier; for kidney tubules, check endogenous peroxidase as a possible DAB artefact (caption: HRP/DAB detection; standard IHC practice).
HPA tissue IHC evidence for BNIP3L
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium 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 |
|---|---|---|---|---|
| Breast | Myoepithelial 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 | Cells in tubules | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Soft tissue | Chondrocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced BNIP3L IHC Tips
Troubleshoot BNIP3L staining in paraffin sections by checking retrieval, cell type and subcellular pattern before comparing chromogenic signal across samples.
What retrieval should I try when BNIP3L staining is weak?
Start with heat-mediated antigen retrieval in EDTA at pH 8.0 for paraffin sections (datasheet M03107). The selected tissue image used that retrieval before overnight incubation with the catalog antibody at 1:50 and 4°C (datasheet M03107). If staining remains weak, compare retrieval duration on adjacent sections while holding antibody concentration and DAB development constant, and watch for tissue damage (standard IHC practice). Judge improvement in the expected granular cytoplasmic pattern, using a matched positive control such as kidney tubular cells rather than increased diffuse color alone (HPA: granular cytoplasmic expression; HPA: High in kidney tubular cells).
Could fixation explain inconsistent BNIP3L staining between paraffin blocks?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative or fixation time (datasheet M03107). For new material, document time to fixation, fixative and fixation duration, then process comparison samples together (standard IHC practice). A routine 10% neutral buffered formalin workflow can provide a consistent starting point, but its suitability for this antibody must be checked with matched tissue controls (standard IHC practice). When comparing existing blocks, keep EDTA retrieval at pH 8.0 and antibody incubation constant, and interpret a weak block cautiously if its fixation history differs (datasheet M03107; standard IHC practice).
Is nuclear or diffuse staining compatible with BNIP3L localisation?
Expect predominantly granular cytoplasmic staining in tissue sections, consistent with mitochondrial enrichment (HPA: tissue IHC profile; HPA: mitochondria enhanced). BNIP3L is annotated at the mitochondrial outer membrane, endoplasmic reticulum and nuclear envelope; nuclear speckles are an additional IF localisation (UniProt O60238 localisation; HPA: nuclear speckles supported). At chromogenic IHC resolution, score granular cytoplasmic signal separately from uniform nuclear or diffuse cytoplasmic color rather than assigning individual organelles from DAB alone (standard IHC practice). Compare the pattern in kidney tubular cells, reported High, with chondrocytes, reported Not detected, while checking that the same compartment is stained in each section (HPA: tissue IHC).
How could isoforms or epitope position alter the staining pattern?
BNIP3L has 2 annotated isoforms and one transmembrane segment at residues 188–208 (UniProt O60238 isoforms and topology). The selected caption does not map the catalog antibody’s epitope, so it cannot establish which isoforms or membrane-facing surfaces that antibody detects (datasheet M03107; UniProt O60238 topology). Ask for an immunogen or epitope map before interpreting loss of staining as loss of all BNIP3L protein, and compare sections processed with identical EDTA pH 8.0 retrieval (standard IHC practice; datasheet M03107). Phosphoserines at residues 62, 117, 118, 120 and 166 are annotated, but epitope overlap and any effect on this stain are unestablished (UniProt O60238 modified residues; datasheet M03107).
How should I adapt the BNIP3L question to multiplex IF?
Pair BNIP3L with a marker identifying the cell population under study, such as kidney tubular cells, whose BNIP3L tissue staining is reported High (HPA: kidney tubular cells). Choose spectrally separated fluorophores and consider a far-red BNIP3L channel when specimen autofluorescence obscures shorter wavelengths; include single-color and unstained controls (standard IF practice). Because BNIP3L crosses a membrane at residues 188–208 and this antibody’s epitope side is unspecified, establish epitope accessibility before setting detergent permeabilisation, then keep that treatment consistent across samples (UniProt O60238 topology; datasheet M03107; standard IF practice). Compare punctate signal with mitochondrial staining, while treating nuclear speckles as a reported additional localisation (HPA: mitochondria enhanced; HPA: nuclear speckles supported).
What should I check when DAB background masks BNIP3L?
First compare a no-primary section with the stained section to identify signal from detection reagents or endogenous peroxidase (standard IHC practice). The selected paraffin-section image used 10% goat-serum blocking, primary antibody at 1:50 overnight at 4°C, and a peroxidase-linked secondary for 30 minutes at 37°C (datasheet M03107). For new runs, check peroxidase blocking, washing and DAB development time while keeping EDTA retrieval at pH 8.0 constant (standard IHC practice; datasheet M03107). A useful endpoint preserves granular cytoplasmic contrast without making unstained spaces or the no-primary section brown (HPA: tissue IHC profile; standard IHC practice).
How should BNIP3L IHC signal be scored across samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and cytoplasmic compartment before scoring, because tissue IHC commonly shows granular cytoplasmic BNIP3L staining (HPA: tissue IHC profile). An H-score combines the percentage of cells at each intensity from 0–3, giving a 0–300 range; record percentage positive separately if intensity is unreliable (standard IHC practice). For area-based analysis, report positive-cell density per mm² of viable tissue or normalise positive cells to the number of eligible cells, using identical thresholds and DAB development across sections (standard IHC practice). Keep cell types separate: kidney tubular cells are reported High, whereas liver cholangiocytes are reported Low (HPA: tissue IHC).
How can I distinguish convincing BNIP3L staining from artefact?
A convincing result has reproducible granular cytoplasmic signal in an appropriate cell population, consistent with the tissue IHC profile and mitochondrial enrichment (HPA: tissue IHC profile; HPA: mitochondria enhanced). Kidney tubular cells are reported High and chondrocytes Not detected, so these patterns provide useful context without making every cell in either tissue a definitive control (HPA: tissue IHC). Uniform nuclear color, section-edge staining, necrotic regions and signal on a no-primary section warrant checks for artefact or endogenous peroxidase before biological interpretation (standard IHC practice). Interpret isolated nuclear signal cautiously: nuclear speckles are an additional IF localisation, while tissue IHC is described as predominantly cytoplasmic (HPA: subcellular localisation; HPA: tissue IHC profile).
Boster reagents
Best BNIP3L / BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like IHC Antibodies
The catalog shows BNIP3L IHC images from human liver cancer and kidney tissue, plus IF data from human U2OS cells (catalog image captions).
Real IHC data
Anti-BNIP3L/Nix Rabbit Monoclonal Antibody
Cat # M03107
Real IHC data
Anti-Bnip3L Antibody
Cat # A03107
Real IF data
Anti-BNIP3L Antibody ®
Cat # A03107-3
M03107 shows IHC staining of paraffin-embedded human liver cancer tissue, while A03107 shows IHC staining of human kidney tissue (catalog: M03107 and A03107 IHC captions). A03107-3 shows IF staining of human U2OS cells and lists ICC/IF among its applications (catalog: A03107-3 IF caption and applications).
Which to pick: For paraffin tissue IHC, choose rabbit monoclonal M03107: its image shows staining after EDTA pH 8 retrieval at 1:50, but does not report the fixative (catalog: M03107 clone and IHC caption). A03107 provides a human kidney IHC example at 2 μg/mL; for IF/ICC, A03107-3 shows human U2OS cells stained at 5 μg/mL (catalog: A03107 IHC caption; A03107-3 IF caption). For mouse or rat work, M03107 lists IHC and mouse/rat reactivity, while A03107-3 lists IF/ICC and mouse/rat reactivity; their displayed images use human samples (catalog: applications, reactivity and image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry O60238 (BNI3L_HUMAN, BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like).
- Human Protein Atlas. BNIP3L tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. BNIP3L subcellular location (ICC-IF): Mainly localized to the mitochondria. In addition localized to the nuclear speckles..
- Human Protein Atlas. BNIP3L antibody validation summary (2 antibodies).
- Expression and Clinical Significance of BCL2 Interacting Protein 3 Like in Multiple Myeloma. Technology in cancer research & treatment 2021 — PMC8258758.
- Gene expression profiling of liver metastases and tumour invasion in pancreatic cancer using an orthotopic SCID mouse model. British journal of cancer 2007 — PMC2360231.
- EPAS1 induction drives myocardial degeneration in desmoplakin-cardiomyopathy. iScience 2025 — PMC11872638.
- BNIP3L promotes cardiac fibrosis in cardiac fibroblasts through [Ca(2+)](i)-TGF-β-Smad2/3 pathway. Scientific reports 2017 — PMC5432493.
- PubMed PMID:9523198 — UniProt-cited evidence.
- PubMed PMID:9867803 — UniProt-cited evidence.
- PubMed PMID:10381623 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for BNIP3L (BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like). Expected localisation Observed cytoplasm (HPA tissue IHC); mitochondrial outer membrane (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet M03107). Validated IHC antibody: M03107 at 1:50 (the product's own IHC validation image is shown). Controls (HPA): positive Breast (Myoepithelial cells); negative Soft tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet M03107); 2. Fixation: Image fixative and duration unreported (datasheet M03107); 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 retrieval: EDTA pH 8.0 (datasheet M03107); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet M03107); 8. Primary antibody: Rabbit monoclonal (clone ABIB-2) anti-BNIP3L, 1:50 (datasheet M03107); 9. Primary incubation: Overnight at 4 °C (datasheet M03107). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image M03107); Caveat: Chondrocytes show no detectable staining (HPA tissue IHC); Isoform / epitope: Two isoforms; antibody epitope coverage is unspecified (UniProt); Regulation: PPTC7 interaction promotes degradation (UniProt). Evidence: UniProt O60238, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to the mitochondria. In addition localized to the…, Datasheet M03107, PMC8258758, PMC2360231. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/BNIP3L/immunohistochemistry-ihc-guide.