PBRM1 / Protein polybromo-1 · IHC design guide

Design Immunohistochemistry for PBRM1

Plan PBRM1 paraffin IHC around its expected nuclear location (UniProt). This guide highlights the observed nuclear and cytoplasmic tissue staining, a high-staining colon gland control, and uncertainty in the tissue profile (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for PBRM1 (IHC for PBRM1): expected localisation Nuclear expected; nuclear and cytoplasmic staining observed (UniProt; HPA tissue IHC), antibody M01130, validated IHC image, and IHC protocol steps
Printable PBRM1 IHC protocol sheet — expected localisation Nuclear expected; nuclear and cytoplasmic staining observed (UniProt; HPA tissue IHC), antibody M01130, controls and protocol steps. Open the full PBRM1 IHC guide →

PBRM1 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 expected; nuclear and cytoplasmic staining observed (UniProt; HPA tissue IHC)
Staining pattern Nuclear/cytoplasmic staining in most tissues; high in colon glands (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet M01130)
Positive control ⓘ Cerebral cortex+4 more · see all
Negative control ⓘ Liver+3 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep fixation consistent across sections. (standard IHC practice; not target-specific)
Caveat Low staining/RNA concordance limits tissue expectations (HPA tissue IHC)
Regulation Widely expressed; low tissue specificity (UniProt; HPA tissue IHC)
Isoform / epitope 9 isoforms; isoform-specific staining cannot be assumed (UniProt)
Section 1

Recommended PBRM1 IHC & IF Protocols

Use the catalog antibody’s IHC-P protocol (datasheet: M01130) alongside the published PBRM1 IHC workflows below (PMC5552448; PMC8870106; PMC6434066).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded mouse thymus tissue; fixative not specified (datasheet M01130)
FixationImage fixative and duration unreported (datasheet M01130); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet M01130); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet M01130)
Primary antibodyRabbit monoclonal (clone AFHG-16) anti-PBRM1, 1:50 (datasheet M01130)
Primary incubationOvernight at 4 °C (datasheet M01130)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet M01130)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultPBRM1-positive staining in neuronal cells of cerebral cortex (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic and nuclear expression in most tissues. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet: M01130); the published workflows below describe other retrieval conditions where stated (PMC5552448; PMC6434066).
Section 2

What Is the Expected PBRM1 Staining Pattern?

PBRM1 is a nuclear chromatin regulator with no transmembrane segment (UniProt Q86U86: location, function, topology). Expect staining in nuclei across many cell types, including glandular cells in colon and duodenum and neurons in cerebral cortex (HPA tissue IHC: High). HPA also reports cytoplasmic staining in most tissues, but rates its tissue IHC profile Uncertain because antibody staining and RNA expression show low consistency (HPA tissue IHC: profile, reliability).

What am I looking at on my slide?
Distinct nuclear staining in colon or duodenal glandular cells, with readable tissue structure and limited background.This fits the expected compartment and two reported high staining cell populations (UniProt Q86U86: nucleus; HPA tissue IHC: High in colon and duodenal glandular cells). Interpret intensity relative to controls on the same run; HPA's tissue IHC reliability is Uncertain, so appearance alone does not establish antibody specificity (HPA tissue IHC: reliability; general IHC practice).
Strong cytoplasmic staining with little or no nuclear staining in an otherwise intact section.An exclusively cytoplasmic result conflicts with UniProt's nuclear location and HPA's nucleoplasmic IF localization (UniProt Q86U86: nucleus; HPA subcellular ICC-IF: nucleoplasm). HPA does report cytoplasmic as well as nuclear tissue staining, so cytoplasmic signal alone is not proof of an artefact (HPA tissue IHC: profile). Check controls and detection background before assigning it to PBRM1 (general IHC practice).
Prominent staining in hepatocytes or prostate glandular cells.These cell populations were reported as not detected in the supplied HPA tissue IHC examples (HPA tissue IHC: liver hepatocytes; prostate glandular cells). Unexpected signal may reflect cross-reactivity or endogenous detection activity; compare a no-primary control and the expected nuclear pattern (general IHC practice; UniProt Q86U86: nucleus). HPA's Uncertain reliability prevents treating either tissue as a definitive negative control (HPA tissue IHC: reliability).
Diffuse chromogen across nuclei, cytoplasm, and tissue spaces, obscuring cell boundaries.A poorly resolved deposit cannot support a compartment-specific PBRM1 call (UniProt Q86U86: nucleus; general IHC practice). Consider nonspecific primary or secondary binding, endogenous detection activity, or excessive development as general IHC causes; use appropriate controls to identify the source (general IHC practice). HPA tissue staining levels do not diagnose the cause of background (HPA tissue IHC: profile).
No visible nuclear signal in colon or duodenal glandular cells.These are reasonable positive-control candidates because HPA reports High staining there, although its tissue IHC reliability is Uncertain (HPA tissue IHC: colon and duodenum, reliability). First check that the section and detection controls worked, then review the catalog antibody's IHC-P instructions and the run conditions (general IHC practice). A blank section alone cannot distinguish technical failure from a true negative result (general IHC practice).
💡Expected PBRM1 appearanceCall a result consistent with PBRM1 when nuclei are clearly stained in expected cells, such as high staining colon glandular cells; isolated intense cytoplasmic staining or diffuse tissue-wide deposit is suspect and needs controls (UniProt Q86U86: nucleus; HPA tissue IHC: colon High, cytoplasmic and nuclear profile, Uncertain reliability; general IHC practice).
How each factor affects the staining
Tissue and cell selectionHPA reports High staining in colon and duodenal glandular cells and cerebral cortex neurons, but not detected in liver hepatocytes or prostate glandular cells (HPA tissue IHC). These are comparative examples, not guaranteed control outcomes: the overall tissue IHC reliability is Uncertain (HPA tissue IHC: reliability).
Antibody validationHPA015629 is rated Uncertain for IHC and Enhanced for ICC; HPA059373 has no supplied IHC rating and is Enhanced for ICC (HPA antibodies). An ICC rating cannot establish performance in paraffin-section chromogenic IHC (HPA antibodies; general IHC practice).
Protein forms and epitope coverageUniProt lists 9 PBRM1 isoforms and a single 1–1689 protein chain, with no signal peptide, propeptide, or transmembrane segment (UniProt Q86U86: isoforms, processing, topology). The supplied evidence gives no antibody epitope, so coverage of individual isoforms cannot be predicted (UniProt Q86U86; HPA antibodies).
IF/ICC Q&A: where should signal appear?In IF/ICC, expect nucleoplasmic localization according to HPA, consistent with UniProt's nuclear assignment (HPA subcellular ICC-IF: nucleoplasm; UniProt Q86U86: nucleus). HPA lists RT-4, U-251MG, and U2OS as image-bearing cell lines; this localization reference does not supply an IF protocol or validate the IHC result (HPA subcellular ICC-IF; HPA antibodies).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
No signal in a chosen high staining tissue.The cause is unresolved from appearance alone; reagent, detection, section, or run conditions may have failed (general IHC practice). HPA's High rating is an observation with Uncertain overall tissue IHC reliability (HPA tissue IHC: reliability).Check the run's positive and no-primary controls, then follow the catalog antibody's IHC-P instructions for retrieval, dilution, and detection (general IHC practice). Do not infer a PBRM1-specific fixation defect from this result.
Only cytoplasmic signal is visible.This lacks the nuclear component expected from UniProt and HPA ICC-IF, although HPA tissue IHC reports mixed nuclear and cytoplasmic expression (UniProt Q86U86: nucleus; HPA subcellular ICC-IF: nucleoplasm; HPA tissue IHC: profile).Inspect counterstained nuclei, compare expected positive cells, and review no-primary background (general IHC practice). Record the discordance rather than scoring cytoplasmic signal alone as confirmed PBRM1.
Chromogen appears in reported negative cell populations.Hepatocytes and prostate glandular cells are listed as not detected by HPA; cross-reactivity or endogenous detection activity is possible (HPA tissue IHC: liver, prostate; general IHC practice). HPA's Uncertain reliability limits the strength of this comparison (HPA tissue IHC: reliability).Compare a no-primary control and an expected positive tissue in the same run; investigate endogenous detection activity if the no-primary control stains (general IHC practice).
Diffuse background obscures nuclear boundaries.Nonspecific binding, endogenous detection activity, or excessive chromogen development can produce background in chromogenic IHC (general IHC practice). The supplied PBRM1 sources do not identify which cause applies.Review blocking, washes, antibody dilution, and development time against the validated IHC-P workflow; compare no-primary and positive controls (general IHC practice).
IF/ICC looks nucleoplasmic, but IHC is weak or atypical.HPA's ICC ratings are Enhanced, while HPA015629's IHC rating is Uncertain and HPA059373 has no supplied IHC rating (HPA antibodies). The assays have different validation evidence (HPA antibodies).Judge the paraffin-section result with IHC controls and the catalog antibody's IHC-P instructions (general IHC practice). Use the IF/ICC finding only as a localization comparison (HPA subcellular ICC-IF: nucleoplasm).
Staining varies between tissues or cell populations.HPA reports High, Low, and not-detected examples despite low tissue RNA specificity and widely expressed PBRM1 (HPA tissue IHC: staining levels, RNA specificity; UniProt Q86U86: tissue specificity). HPA tissue IHC reliability is Uncertain (HPA tissue IHC: reliability).Score the relevant cell population and nuclear compartment separately, alongside same-run controls; avoid treating whole-section intensity as a single result (UniProt Q86U86: nucleus; general IHC practice).

Sample controls for PBRM1 IHC & IF

🧪Run colon first: glandular cells should show nuclear staining (HPA: High in colon glandular cells; UniProt: Nucleus). Use liver hepatocytes as the negative tissue (HPA: Not detected in hepatocytes); on the colon slide, cells without nuclear chromogen provide a visual background check, but the supplied HPA rows do not identify a specific internal negative cell type.
Positive control tissue: Cerebral cortex (Neuronal cells, HPA High)
Negative control tissue: Liver (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PBRM1 in RT-4, U-251MG, U2OS, with annotated localisation: Nucleoplasm (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only section; an isotype control matched to the rabbit antibody’s host and clonality (selected-SKU caption: rabbit primary); and, if available, a PBRM1-knockout specimen as a biological negative. Quench endogenous peroxidase and check for residual background in the colon section before interpreting HRP–DAB staining (selected-SKU caption: HRP–DAB detection).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the fixative in the M01130 paraffin-section caption is unreported (selected-SKU caption: fixative not stated). The caption uses heat retrieval in EDTA at pH 8.0, but supplies no comparison with unretrieved sections, so retrieval dependency needs testing (selected-SKU caption: EDTA retrieval). Frozen sections or IF cannot be judged easier from the supplied evidence; IF/ICC images show nucleoplasmic localization, while endogenous peroxidase remains a potential chromogenic background in the selected colon section (HPA subcellular: Nucleoplasm; selected-SKU caption: HRP–DAB detection).

HPA tissue IHC evidence for PBRM1

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
Cerebral cortex Neuronal cells High Protein (IHC) HPA →
Cervix Glandular cells High Protein (IHC) HPA →
Colon Glandular cells High Protein (IHC) HPA →
Duodenum Glandular cells High Protein (IHC) HPA →
Endometrium Glandular cells High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Liver Hepatocytes Not detected Protein (IHC) HPA →
Ovary Ovarian stroma cells Not detected Protein (IHC) HPA →
Prostate Glandular cells Not detected Protein (IHC) HPA →
Spleen Cells in red pulp Not detected Protein (IHC) HPA →
Section 3

Advanced PBRM1 IHC Tips

These questions focus on nuclear PBRM1 staining in paraffin sections, with one entry on exploratory IF (UniProt Q86U86; datasheet M01130).

How should I retrieve PBRM1 in paraffin sections if nuclear staining is weak?
Use heat-mediated antigen retrieval in EDTA at pH 8.0 for paraffin-section PBRM1 IHC (datasheet M01130). The selected mouse thymus example used this retrieval before 10% goat-serum blocking and a 1:50 primary antibody incubation overnight at 4°C (datasheet M01130). If staining remains weak, compare retrieval duration on matched sections while holding antibody concentration and chromogen development constant; record the heating and cooling conditions for each run (standard IHC practice). Check whether nuclei gain signal without a parallel increase in diffuse cytoplasmic or section-edge staining, because PBRM1 is nuclear and HPA reports uncertain tissue-IHC reliability (UniProt Q86U86 localisation; HPA tissue IHC).
Can I attribute weak PBRM1 IHC to fixation?
Target-specific PBRM1 fixation sensitivity is unknown from the supplied evidence, and the selected paraffin-section caption does not state a fixative (datasheet M01130). Record the fixative, fixation duration, processing history and section age before comparing weak and strong cases, since these variables can affect antigen preservation in routine IHC (standard IHC practice). On matched sections, hold EDTA retrieval at pH 8.0 and the 1:50 primary dilution constant while comparing specimens with documented processing histories (datasheet M01130; standard IHC practice). A difference in nuclear staining under those conditions identifies a processing association, but does not establish a PBRM1-specific fixation mechanism (standard IHC interpretation).
Should cytoplasmic PBRM1 staining count as a positive result?
Prioritise nuclear staining when assessing PBRM1: UniProt places the protein in the nucleus, and HPA IF localises it to the nucleoplasm (UniProt Q86U86 localisation; HPA subcellular). HPA tissue IHC also describes cytoplasmic and nuclear staining across most tissues, but grades that IHC profile Uncertain because staining and RNA expression have low consistency (HPA tissue IHC). Score nuclear and cytoplasmic compartments separately rather than merging them into one positive category, and inspect the same cell type across comparable regions (standard IHC practice). Treat isolated cytoplasmic signal as provisional until it survives antibody and detection controls and agrees with an independent assay (standard IHC interpretation).
Could PBRM1 isoforms or epitope masking explain variable nuclear staining?
PBRM1 has 9 listed isoforms and 6 bromodomains, so an antibody's epitope position matters when interpreting differences between specimens (UniProt Q86U86 isoforms and domains). The supplied M01130 caption gives an IHC dilution and retrieval method but does not identify its epitope, so isoform coverage cannot be assigned from that caption (datasheet M01130). Check the antibody's documented immunogen or epitope against the isoforms relevant to the experiment before treating absent staining as absent PBRM1 (UniProt Q86U86 isoforms; standard IHC interpretation). If coverage remains unknown, compare independent antibodies with documented, distinct epitopes on matched sections and retain EDTA pH 8.0 as the starting retrieval condition (datasheet M01130; standard IHC practice).
How can I investigate PBRM1 localisation by IF alongside cell-type markers?
For exploratory IF, pair PBRM1 with a validated marker of the expected cell type and a nuclear counterstain, then inspect signal within individual nuclei (HPA subcellular; standard IF practice). Choose well-separated fluorophores and place the weaker signal in a channel with lower tissue autofluorescence; include single-stain and unstained controls to assess bleed-through and background (standard IF practice). PBRM1 is nuclear and has no transmembrane segment, so permeabilisation should allow access across the plasma and nuclear envelopes to the nuclear epitope, whose precise position is not supplied (UniProt Q86U86 topology and localisation; standard IF practice). Optimise IF fixation and permeabilisation with IF controls rather than borrowing the paraffin-section retrieval or incubation conditions as an IF protocol (datasheet M01130; standard IF practice).
How do I distinguish PBRM1 signal from DAB background?
The selected paraffin-section example used 10% goat serum, a 1:50 rabbit primary overnight at 4°C, a peroxidase-conjugated secondary for 30 minutes at 37°C, and DAB development (datasheet M01130). For troubleshooting, include a no-primary control and a peroxidase-blocked section; peroxidase blocking is a general chromogenic IHC step, not PBRM1-specific validation (standard IHC practice). Compare background in those controls with staining in intact nuclei, and shorten chromogen development or adjust antibody concentration if diffuse colour obscures cellular boundaries (UniProt Q86U86 localisation; standard IHC practice). Document counterstain intensity and examine section edges separately, where handling and reagent pooling can complicate interpretation (standard IHC practice).
What is a defensible way to quantify PBRM1 IHC across specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Define the scored cell population and count evaluable nuclei within comparable tissue regions, because PBRM1 is a nuclear protein (UniProt Q86U86 localisation; standard IHC practice). Report the percentage of positive nuclei and, when intensity categories are reproducible, a nuclear H-score from 0–300 using the percentages at intensity grades 0–3 (standard IHC practice). Normalise counts to the number of evaluable cells, or report positive-cell density per mm² when tissue area is the denominator; state the chosen denominator for every specimen (standard IHC practice). Apply the same positivity threshold, exclusion rules and DAB development conditions throughout, and report cytoplasmic staining separately because HPA tissue-IHC reliability is uncertain (HPA tissue IHC; standard IHC practice).
When is apparent PBRM1 loss or positivity likely to be artefactual?
Interpret convincing PBRM1 positivity as staining within intact nuclei of the scored cell type, consistent with its nuclear and nucleoplasmic localisation (UniProt Q86U86 localisation; HPA subcellular). Recheck signal concentrated at section edges, in necrotic areas, outside the expected cell population or in a no-primary control before calling a case positive (standard IHC practice). Check a peroxidase-blocked control when DAB signal could reflect endogenous enzyme activity, since the selected example used peroxidase detection and DAB (datasheet M01130; standard IHC practice). For apparent loss, verify preserved morphology and a suitable internal or external positive control; HPA's Uncertain tissue-IHC reliability makes isolated negative staining insufficient to establish biological absence (HPA tissue IHC; standard IHC interpretation).
Boster reagents

Best PBRM1 / Protein polybromo-1 IHC Antibodies

The catalog lists human, mouse and rat reactivity for two anti-PBRM1 antibodies (catalog applications/reactivity); M01130 has a mouse thymus paraffin-section IHC image (M01130 image caption).

Real IHC data IHC analysis of PBRM1 using anti-PBRM1 antibody (M01130). PBRM1 was detected in a paraffin-embedded section of mouse thymus tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1:50 rabbit anti-PBRM1 Antibody (M01130) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-PBRM1 Rabbit Monoclonal Antibody
Cat # M01130

M01130 renders with a chromogenic IHC image of mouse thymus in a paraffin section; IHC and IF/ICC are listed applications, and human, mouse and rat are listed reactivities (M01130 image caption; catalog applications/reactivity). A01130-1 is listed for IF/ICC with human, mouse and rat reactivity, but has no IHC application or IHC/IF image in the supplied catalog (A01130-1 catalog applications/reactivity/images).

Which to pick: Choose M01130 for paraffin-section tissue IHC: its own image caption documents mouse thymus, EDTA retrieval at pH 8.0 and a 1:50 primary dilution; the fixative is unreported (M01130 image caption). For IF/ICC, A01130-1 has a listed IF concentration of 5 μg/ml for human samples, while M01130 lists IF/ICC and a 1:50 IF dilution (A01130-1 dilution data; M01130 catalog applications/dilution). For work across human, mouse and rat, both list those species, but M01130 is the rabbit monoclonal with an IHC application and a mouse tissue IHC image (catalog host/clone/applications/reactivity; M01130 image caption).

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

References

  1. UniProt Consortium. UniProt entry Q86U86 (PB1_HUMAN, Protein polybromo-1).
  2. Human Protein Atlas. PBRM1 tissue IHC expression (reliability: Uncertain).
  3. Human Protein Atlas. PBRM1 subcellular location (ICC-IF): Localized to the nucleoplasm..
  4. Human Protein Atlas. PBRM1 antibody validation summary (2 antibodies).
  5. PBRM1 loss is a late event during the development of cholangiocarcinoma. Histopathology 2017 — PMC5552448.
  6. PBRM1 Immunohistochemical Expression Profile Correlates with Histomorphological Features and Endothelial Expression of Tumor Vasculature for Clear Cell Renal Cell Carcinoma. Cancers 2022 — PMC8870106.
  7. Risk Prediction Tool for Aggressive Tumors in Clinical T1 Stage Clear Cell Renal Cell Carcinoma Using Molecular Biomarkers. Computational and structural biotechnology journal 2019 — PMC6434066.
  8. Role of the Pbrm1 subunit and the PBAF complex in Schwann cell development. Scientific reports 2022 — PMC8850583.
  9. PubMed PMID:11078522 — UniProt-cited evidence.
  10. PubMed PMID:12487023 — UniProt-cited evidence.
  11. PubMed PMID:15735765 — UniProt-cited evidence.