UBQLN4 / Ubiquilin-4 · IHC design guide

Design Immunohistochemistry for UBQLN4

Plan chromogenic FFPE staining around UBQLN4’s general nuclear tissue pattern (HPA tissue IHC). The catalog antibody A08887 has an IHC dilution of 1:100–1:300 (datasheet: A08887); respiratory epithelial and rectal glandular cells show high staining (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for UBQLN4 (IHC for UBQLN4): expected localisation Predominantly nuclear in tissue sections (HPA tissue IHC), antibody A08887, validated IHC image, and IHC protocol steps
Printable UBQLN4 IHC protocol sheet — expected localisation Predominantly nuclear in tissue sections (HPA tissue IHC), antibody A08887, controls and protocol steps. Open the full UBQLN4 IHC guide →

UBQLN4 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 Predominantly nuclear in tissue sections (HPA tissue IHC)
Staining pattern General nuclear staining across cell types (HPA tissue IHC)
Antigen retrieval Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen)
Positive control ⓘ Bronchus+4 more · see all
Negative control ⓘ Heart muscle+1 more · see all
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 A08887)
Caveat Cardiomyocytes may lack staining despite reported heart expression (HPA tissue IHC; UniProt)
Regulation DNA damage drives nuclear recruitment (UniProt)
Isoform / epitope 2 isoforms; epitope coverage is unresolved (UniProt)
Section 1

Recommended UBQLN4 IHC & IF Protocols

The catalog antibody’s IHC-P protocol is followed by published UBQLN4 IHC conditions from two articles (PMC8637560; PMC8688525).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human colon carcinoma tissue; fixative not specified (datasheet A08887)
FixationImage fixative and duration unreported (datasheet A08887); 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 anti-UBQLN4, 1:100 - 1:300 (datasheet A08887)
Primary incubationOvernight at 4 °C (standard)
DetectionHRP-polymer secondary, DAB chromogen 5–10 min (standard)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultUBQLN4-positive staining in respiratory epithelial cells of bronchus (HPA tissue IHC: High). HPA tissue profile: General nuclear expression. No signal in the no-primary control.
💡Decision noteStart with Tris-EDTA pH 9.0 retrieval at 95–98 °C for 20 min (page retrieval rule: nuclear antigen); neither article excerpt specifies retrieval.
Section 2

What Is the Expected UBQLN4 Staining Pattern?

UBQLN4 staining is expected mainly in nuclei across tissues (HPA tissue IHC: general nuclear expression), with High staining reported in respiratory epithelial, rectal glandular and urothelial cells (HPA tissue IHC). Nucleoplasmic localization is supported by ICC-IF (HPA ICC-IF). UniProt also lists cytoplasmic and other intracellular locations; UBQLN4 has no transmembrane segment (UniProt Q9NRR5 topology). HPA rates the tissue IHC pattern Approved, with medium consistency against RNA data (HPA tissue IHC).

What am I looking at on my slide?
Distinct nuclear chromogen in respiratory epithelial cells of bronchus or nasopharynx, rectal glandular cells, or urothelial cells.This matches the reported High staining in those cell populations and the general nuclear pattern (HPA tissue IHC). Assess signal within the named cells, rather than treating every cell in the section as an equally strong positive; tissue architecture helps distinguish nuclear staining from pigment or deposits (general IHC practice).
Predominantly extracellular, luminal or sharply cell-surface staining, with little nuclear signal.That distribution conflicts with the HPA nuclear IHC pattern and the absence of a UBQLN4 transmembrane segment (HPA tissue IHC; UniProt Q9NRR5 topology). Review morphology and controls for nonspecific staining or detection deposits (general IHC practice). Cytoplasmic signal alone needs more careful interpretation because UniProt also lists cytoplasmic locations (UniProt Q9NRR5).
Strong staining in cardiomyocytes or cholangiocytes, especially when expected positive cells are unstained.HPA reports UBQLN4 as Not detected in those specific cell populations (HPA tissue IHC). Check cell identification and reagent controls before attributing the signal to UBQLN4: cross-reactivity or endogenous detection activity can produce staining in unexpected cells (general IHC practice). A single discrepant section does not establish a new tissue pattern.
Uniform chromogen across nuclei, cytoplasm, stroma and empty spaces, obscuring cell boundaries.This is diffuse background rather than an interpretable cell-specific nuclear pattern (HPA tissue IHC; general IHC practice). Check the reagent-free and primary-omission controls, detection chemistry, washing and chromogen development (general IHC practice). Do not score broadly colored tissue as UBQLN4-positive merely because some nuclei are included.
No nuclear signal in a bronchus, nasopharynx, rectum or urinary bladder section selected as a positive control.The relevant epithelial, glandular or urothelial cells are reported High by HPA, so absent staining warrants a workflow check (HPA tissue IHC). First confirm that those cells are present and preserved, then inspect control performance, antibody application and detection (general IHC practice). HPA's Approved rating still carries only medium staining-to-RNA consistency (HPA tissue IHC).
💡Expected UBQLN4 appearanceCall a section positive when the named respiratory epithelial, rectal glandular or urothelial cells show clear, predominantly nuclear High staining (HPA tissue IHC); widespread extracellular or cell-surface color without that pattern is suspect (UniProt Q9NRR5 topology; general IHC practice).
How each factor affects the staining
Tissue and cell selectionHPA reports High staining in respiratory epithelial cells of bronchus and nasopharynx, rectal glandular cells, and urothelial cells; cardiomyocytes and cholangiocytes are Not detected (HPA tissue IHC). Compare identified cell populations, not whole-organ labels. UniProt describes high expression in heart and skeletal muscle, while HPA reports cardiomyocytes as undetected and myocytes as low by IHC; these observations use different readouts (UniProt Q9NRR5; HPA tissue IHC).
Antibody evidenceThe supplied HPA antibody, HPA061797, has IHC status Approved and ICC status Supported (HPA antibodies). HPA describes tissue IHC as having medium consistency with RNA expression (HPA tissue IHC). Use that evidence to set confidence in the reported pattern; it does not turn an unexpected compartment or cell type into a validated positive.
Intracellular distributionThe predominant tissue interpretation is nuclear, and ICC-IF supports nucleoplasmic localization (HPA tissue IHC; HPA ICC-IF). UniProt additionally lists cytoplasm, chromosome, endoplasmic reticulum, perinuclear region and autophagosomes; it reports nuclear recruitment after DNA damage (UniProt Q9NRR5). Those annotations allow context-dependent intracellular patterns, but they do not establish the frequency or intensity of each pattern in routine tissue IHC.
Protein form and epitope limitsUniProt lists 2 isoforms, a single 1–601 chain, no signal peptide, no propeptide and no transmembrane segment (UniProt Q9NRR5). Without an antibody epitope or isoform-specific validation in the supplied evidence, the staining cannot be assigned to one isoform; the record also gives no basis for interpreting extracellular staining as normal UBQLN4 shedding.
Phosphorylation and damage responseUniProt records phosphorylation at Ser-318 by ATM and recruitment to nuclear DNA-damage sites after damage (UniProt Q9NRR5). This supports a possible change in localization under that condition. The supplied evidence does not show whether the IHC antibody recognizes phosphorylated and unphosphorylated UBQLN4 equally, so staining intensity cannot be read as a phosphorylation assay.
IF/ICC Q&A: what should a separate IF result show?A mainly nucleoplasmic signal is the supported ICC-IF expectation; HPA lists images from MCF-7 and U2OS (HPA ICC-IF). UniProt's additional intracellular locations may be context-dependent (UniProt Q9NRR5). This IHC interpretation does not specify an IF/ICC protocol.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Expected positive cells are present but their nuclei are unstained.The observed result conflicts with HPA's High calls for the specified epithelial, glandular or urothelial cells (HPA tissue IHC); a staining or detection failure is possible (general IHC practice).Verify the cell identity and positive control, then check that the primary antibody, antigen-retrieval step and detection reagents were applied as intended (general IHC practice). The supplied sources give no UBQLN4-specific retrieval condition or fixation-sensitivity claim.
Chromogen spreads across stroma or empty spaces.Diffuse color lacks the cell-associated nuclear distribution reported by HPA and can reflect background or detection deposits (HPA tissue IHC; general IHC practice).Compare primary-omission and reagent controls; review washing, blocking and chromogen development using standard IHC controls (general IHC practice). Score only interpretable staining in identified cells.
Unexpected strong signal appears in cardiomyocytes or cholangiocytes.Both are Not detected in the supplied HPA IHC observations (HPA tissue IHC); misidentified cells, cross-reactivity or endogenous detection activity are possible explanations (general IHC practice).Recheck morphology and control sections. If using an enzyme-based detection system, assess its relevant endogenous activity with an appropriate control before assigning UBQLN4 positivity (general IHC practice).
The slide shows only cytoplasmic or perinuclear staining.UniProt includes those locations, but HPA describes general nuclear tissue staining and supported nucleoplasmic ICC-IF staining (UniProt Q9NRR5; HPA tissue IHC; HPA ICC-IF).Confirm that nuclei are identifiable by counterstain and compare positive and negative controls (general IHC practice). Record the compartment explicitly; do not treat an exclusively cytoplasmic pattern as matching the dominant HPA IHC pattern.
Nearly every cell looks equally strong, including HPA low or undetected populations.Uniform intensity conflicts with HPA's cell-specific range, from High in selected epithelia to low in myocytes and undetected in cardiomyocytes (HPA tissue IHC).Review exposure to chromogen, background controls and cell-level scoring (general IHC practice). Compare nuclei in the named HPA populations before concluding that the entire tissue is uniformly positive.
A nuclear result differs between specimens or from an IF image.HPA's tissue IHC has medium consistency with RNA data, while ICC-IF supports nucleoplasmic localization; UniProt also documents context-dependent intracellular localization (HPA tissue IHC; HPA ICC-IF; UniProt Q9NRR5).Compare the same cell type and compartment across specimens, document tissue condition and controls, and avoid inferring a fixation effect or phosphorylation state from the discrepancy alone (general IHC practice; UniProt Q9NRR5).

Sample controls for UBQLN4 IHC & IF

🧪Run bronchus first; respiratory epithelial cells should stain (HPA: High in bronchus respiratory epithelial cells), and use liver cholangiocytes as a negative comparator (HPA: Not detected in liver cholangiocytes). On the bronchus slide, cells without specific staining should remain at background level, but the supplied HPA row does not establish which other cell types are truly negative (HPA: bronchus row scores respiratory epithelial cells).
Positive control tissue: Bronchus (Respiratory epithelial cells, HPA High)
Negative control tissue: Heart muscle (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show UBQLN4 in MCF-7, U2OS, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include no-primary and secondary-only controls, a control antibody matched to the primary antibody’s host species, isotype and clonality, and a UBQLN4 knockout or peptide-block control for specificity (standard IHC practice; catalog antibody A08887 caption: synthesized-peptide block). For bronchus chromogenic IHC, quench endogenous peroxidase and check the no-primary section for residual background (standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A08887 paraffin-section caption does not state a fixative (catalog antibody A08887 tissue-IHC caption). Retrieval dependence is unreported; optimize antigen retrieval empirically on matched paraffin sections (catalog antibody A08887 tissue-IHC caption: paraffin-embedded tissue; standard IHC practice). The supplied evidence does not establish whether frozen sections or IF are easier; HPA supports nucleoplasmic ICC-IF localization in MCF-7 and U2OS, while bronchus chromogenic sections warrant a background check for endogenous peroxidase (HPA subcellular: nucleoplasm supported, MCF-7 and U2OS; standard IHC practice).

HPA tissue IHC evidence for UBQLN4

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

TissueCell typeLevelEvidenceSource
Bronchus Respiratory epithelial cells High Protein (IHC) HPA →
Nasopharynx Respiratory epithelial cells High Protein (IHC) HPA →
Rectum Glandular cells High Protein (IHC) HPA →
Urinary bladder Urothelial cells High Protein (IHC) HPA →
Adrenal gland Glandular cells Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Heart muscle Cardiomyocytes Not detected Protein (IHC) HPA →
Liver Cholangiocytes Not detected Protein (IHC) HPA →
Section 3

Advanced UBQLN4 IHC Tips

Troubleshooting for chromogenic UBQLN4 IHC in paraffin sections, with one IF/ICC question for the separate fluorescence workflow.

What should I change when UBQLN4 staining is weak after retrieval?
Start with Tris-EDTA pH 9.0 HIER at 95–98 °C for 20 min (page retrieval setting). Let sections cool in retrieval buffer before washing, and compare a retrieval-treated section with an otherwise identical section on the same run (standard IHC practice). UBQLN4 has a supported nucleoplasmic location, so assess nuclear signal before judging the retrieval ineffective (HPA subcellular: nucleoplasm). If staining remains weak, vary heating time in small steps while keeping antibody concentration and detection conditions fixed, and watch for tissue damage (standard IHC practice). The catalog image shows staining in paraffin-embedded human colon carcinoma with peptide blocking, but reports no retrieval conditions (caption: A08887).
Could fixation explain weak or patchy UBQLN4 staining?
Target-specific fixation sensitivity is unknown; the catalog caption identifies a paraffin section but does not state its fixative (caption: A08887). Record each specimen’s fixative, fixation duration and tissue thickness before comparing UBQLN4 staining across blocks (standard IHC practice). For a controlled comparison, process matched samples under the same fixation conditions and stain their sections together with the same retrieval and detection run (standard IHC practice). Evaluate whether weak areas follow processing boundaries or tissue damage, and check nuclear morphology before changing antibody concentration (standard IHC practice; HPA: general nuclear expression). Do not assign a fixation mechanism from UBQLN4 topology, phosphorylation sites or tissue staining patterns alone (UniProt: no transmembrane segment; phosphosites; HPA tissue IHC).
How should I assess nuclear versus cytoplasmic UBQLN4 staining?
Use the hematoxylin counterstain to identify intact nuclei, then score nuclear and cytoplasmic staining separately in each cell population (standard IHC practice). General nuclear expression in tissue and supported nucleoplasmic localisation provide a reference for routine sections (HPA tissue IHC; HPA subcellular). Cytoplasmic, perinuclear, endoplasmic reticulum and autophagosome localisation are also reported, so reproducible staining outside the nucleus warrants evaluation rather than automatic rejection (UniProt Q9NRR5 subcellular). Compare it with a peptide-blocked section when using A08887, and check whether it survives changes in detection intensity (caption: A08887; standard IHC practice). Nuclear recruitment after DNA damage is a conditional mechanism, not a default expectation for every specimen (UniProt Q9NRR5: ATM Ser-318 response).
Could isoforms or epitope accessibility change my UBQLN4 IHC result?
UBQLN4 has 2 listed isoforms, but the supplied catalog caption does not identify the antibody epitope or establish isoform-specific staining (UniProt Q9NRR5 isoforms; caption: A08887). Ask for the immunogen sequence and align it against both isoforms before interpreting a missing cell population as isoform loss (standard IHC practice). The protein contains an N-terminal ubiquitin-like domain at residues 13–87 and a UBA domain at 553–598, which can guide epitope mapping once the immunogen is known (UniProt Q9NRR5 domains). Ser-318 is phosphorylated by ATM after DNA damage, but phosphorylation-dependent antibody binding is unestablished here (UniProt Q9NRR5 modified residues). Keep retrieval and section processing matched when comparing specimens (standard IHC practice).
How can IF/ICC help check a disputed UBQLN4 IHC pattern?
On the separate IF/ICC workflow, compare UBQLN4 with a marker for the expected cell type and inspect single channels before interpreting overlap (standard IF practice). Select fluorophores away from the specimen’s strongest autofluorescence, and include single-label and no-primary controls to identify bleed-through and background (standard IF practice). UBQLN4 has no transmembrane segment and has a supported nucleoplasmic location, so use permeabilisation compatible with access to intracellular and nuclear epitopes (UniProt Q9NRR5 topology; HPA subcellular; standard IF practice). Compare nuclear and cytoplasmic signal separately, since both compartments are reported (UniProt Q9NRR5 subcellular). HPA lists ICC/IF images in MCF-7 and U2OS, but the supplied evidence gives no fixation or permeabilisation settings to transfer to this workflow (HPA subcellular).
How do I reduce diffuse or misleading UBQLN4 chromogenic background?
Inspect a no-primary section to separate nonspecific detection signal from UBQLN4 antibody staining (standard IHC practice). For a peroxidase and DAB workflow, apply an endogenous peroxidase block and check whether residual pigment appears in the control; these are general IHC steps, not UBQLN4-specific validation (standard IHC practice). Reduce overly concentrated primary antibody or detection reagent one variable at a time, while preserving a positive reference section in the same run (standard IHC practice). Wash consistently and assess whether staining follows section edges, folds or damaged tissue instead of intact nuclei (standard IHC practice; HPA: general nuclear expression). The A08887 peptide-blocked image supports an epitope competition check for that image, not universal specificity across specimens (caption: A08887).
What is a defensible way to quantify UBQLN4 IHC? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, then apply the same thresholds to all sections in a comparison (standard IHC practice). For nuclear staining, report the percentage of positive intact cells and an H-score using intensity grades 0–3; report cytoplasmic staining separately if assessed (standard IHC practice; HPA: general nuclear expression). If counting discrete positive cells, report density per mm² of viable tissue and exclude necrosis, folds and section edges by a prespecified rule (standard IHC practice). Normalise counts to the number of eligible cells or viable tissue area, and compare specimens stained in the same run with the same detection settings (standard IHC practice). HPA reports medium consistency between antibody staining and RNA expression, so avoid treating RNA abundance as a direct staining calibration (HPA tissue IHC).
Which UBQLN4 staining patterns suggest a true positive rather than artefact?
A credible result has reproducible staining in intact cells, a clear compartment assignment and low signal in matched negative controls (standard IHC practice). General nuclear expression and supported nucleoplasmic localisation make nuclear staining a useful reference, while reported cytoplasmic localisation prevents dismissing every cytoplasmic signal (HPA tissue IHC; HPA subcellular; UniProt Q9NRR5 subcellular). Check unexpected cell populations against tissue morphology: HPA reports high staining in rectal glandular cells but no detection in heart cardiomyocytes or liver cholangiocytes (HPA tissue IHC). Edge accentuation, necrotic staining and residual endogenous peroxidase signal should be tested with adjacent morphology and no-primary controls (standard IHC practice). Peptide blocking in the A08887 colon carcinoma image supports that image’s comparison, but does not establish the identity of every stained cell elsewhere (caption: A08887).
Boster reagents

Best UBQLN4 / Ubiquilin-4 IHC Antibodies

Catalog IHC images cover human colon carcinoma paraffin sections and mouse kidney tissue (image captions); IF/ICC is listed for A08887, with no IF image supplied (catalog payload).

Real IHC data Immunohistochemistry analysis of paraffin-embedded human colon carcinoma tissue, using UBQLN4 Antibody. The picture on the right is blocked with the synthesized peptide.
Anti-UBQLN4/A1Up Antibody
Cat # A08887
Real IHC data Immunohistochemistry of CIP75 in mouse kidney tissue with CIP75 antibody at 5 μg/mL.
Anti-CIP75 UBQLN4 Antibody
Cat # A08887-1

A08887 has an IHC image of human colon carcinoma paraffin sections with a peptide-blocked comparison; its applications include IF and ICC, and its listed reactivity is human and mouse (A08887 image caption; catalog). A08887-1 has an IHC image of mouse kidney tissue at 5 μg/mL; its applications include IHC-P, and its listed reactivity is human, mouse and rat (A08887-1 image caption; catalog).

Which to pick: For human tissue IHC on paraffin sections, choose A08887 based on its own colon carcinoma image; the fixative is unreported (A08887 image caption). For IF/ICC, choose A08887 because those applications are listed, although no IF image is supplied (A08887 catalog payload). For mouse kidney IHC, A08887-1 has direct image evidence; it also lists rat reactivity, but its supplied IHC validation is in mouse tissue (A08887-1 image caption; catalog).

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

References

  1. UniProt Consortium. UniProt entry Q9NRR5 (UBQL4_HUMAN, Ubiquilin-4).
  2. Human Protein Atlas. UBQLN4 tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. UBQLN4 subcellular location (ICC-IF): Localized to the nucleoplasm..
  4. Human Protein Atlas. UBQLN4 antibody validation summary (1 antibodies).
  5. UBQLN4 is an ATM substrate that stabilizes the anti-apoptotic proteins BCL2A1 and BCL2L10 in mesothelioma. Molecular oncology 2021 — PMC8637560.
  6. A Comprehensive Multiomics Analysis Identified Ubiquilin 4 as a Promising Prognostic Biomarker of Immune-Related Therapy in Pan-Cancer. Journal of oncology 2021 — PMC8443395.
  7. The UbL-UBA Ubiquilin4 protein functions as a tumor suppressor in gastric cancer by p53-dependent and p53-independent regulation of p21. Cell death and differentiation 2019 — PMC6370890.
  8. UBQLN4 is activated by C/EBPβ and exerts oncogenic effects on colorectal cancer via the Wnt/β-catenin signaling pathway. Cell death discovery 2021 — PMC8688525.
  9. PubMed PMID:11001934 — UniProt-cited evidence.
  10. PubMed PMID:14702039 — UniProt-cited evidence.
  11. PubMed PMID:16710414 — UniProt-cited evidence.