ATG4A / Cysteine protease ATG4A · IHC design guide

Design Immunohistochemistry for ATG4A

Plan paraffin-section ATG4A IHC around the reported cytoplasmic tissue pattern, which awaits external verification (HPA tissue IHC). Human colon glandular cells show high staining (HPA tissue IHC); the catalog antibody A06539-2 has a starting range of 0.5–1 μg/mL (datasheet A06539-2).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for ATG4A (IHC for ATG4A): expected localisation General cytoplasmic tissue staining (HPA tissue IHC), antibody A06539-2, validated IHC image, and IHC protocol steps
Printable ATG4A IHC protocol sheet — expected localisation General cytoplasmic tissue staining (HPA tissue IHC), antibody A06539-2, controls and protocol steps. Open the full ATG4A IHC guide →

ATG4A 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 General cytoplasmic tissue staining (HPA tissue IHC)
Staining pattern Cytoplasmic staining across multiple cell types (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet A06539-2)
Positive control ⓘ Appendix+4 more · see all
Negative control ⓘ Adipose tissue+1 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific)
Caveat Tissue staining awaits external verification (HPA tissue IHC)
Regulation No expression regulation annotated (UniProt)
Isoform / epitope Four isoforms; no propeptide annotated (UniProt)
Section 1

Recommended ATG4A IHC & IF Protocols

The catalog antibody’s IHC-P protocol (datasheet: EDTA pH 8.0) is accompanied by two published paraffin-section IHC protocols (PMC5129932; PMC12234470).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human rectal cancer tissue; fixative not specified (datasheet A06539-2)
FixationImage fixative and duration unreported (datasheet A06539-2); 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 A06539-2); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A06539-2)
Primary antibodyRabbit anti-ATG4A, 0.5-1μg/ml (datasheet A06539-2)
Primary incubationOvernight at 4 °C (datasheet A06539-2)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet A06539-2)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultATG4A-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 (datasheet: EDTA pH 8.0); one published protocol also uses this condition (PMC5129932).
Section 2

What Is the Expected ATG4A Staining Pattern?

ATG4A is a cytoplasmic protein with no transmembrane segment (UniProt Q8WYN0). In paraffin-section IHC, expect cytoplasmic staining in glandular, epithelial, hematopoietic, germinal-center, and kidney tubular cells reported as High by HPA (HPA: tissue IHC). Treat this as a provisional pattern: HPA describes general cytoplasmic expression, but rates its tissue IHC evidence Uncertain, pending external verification (HPA: tissue IHC reliability).

What am I looking at on my slide?
Distinct cytoplasmic staining in colon or appendix glandular cells, with visible cell boundaries.This fits the reported compartment and cell types (UniProt Q8WYN0: Cytoplasm; HPA: High in colon and appendix glandular cells). Score the fraction and intensity in the intended cells, and compare sections processed in the same run (general IHC practice). The HPA tissue pattern remains Uncertain pending external verification (HPA: tissue IHC reliability).
Predominantly nuclear or sharply membrane-restricted staining, with little cytoplasmic signal.That distribution conflicts with the annotated cytoplasmic location and absence of a transmembrane segment (UniProt Q8WYN0). Review the counterstain, morphology, and detection controls before assigning it to ATG4A (general IHC practice). HPA tissue IHC does not validate either pattern as target-specific (HPA: tissue IHC reliability Uncertain).
Strong signal in adipocytes or ovarian stromal cells while nearby expected-positive cells are weak.HPA reports ATG4A as Not detected in those cell types (HPA: adipocytes; ovarian stroma). Investigate cross-reactivity or endogenous detection activity with appropriate controls (general IHC practice). A negative HPA observation is a comparison point, not proof that every specimen of that tissue must remain unstained (HPA: tissue IHC reliability Uncertain).
Uniform haze across cells, stroma, and empty areas, obscuring cell boundaries.A non-cellular distribution cannot support cell-specific scoring (general IHC practice). Check the no-primary control, wash quality, blocking, and chromogen development in the same run (general IHC practice). It does not resemble HPA's reported general cytoplasmic expression (HPA: tissue IHC profile).
No staining in colon glandular cells or kidney tubular cells despite preserved morphology.Both are reported High in HPA tissue IHC (HPA: colon glandular cells; kidney tubular cells). First check that the assay's positive control worked, then review antibody dilution, retrieval, and detection steps (general IHC practice). Absence alone cannot establish true ATG4A loss because HPA rates its tissue IHC evidence Uncertain (HPA: tissue IHC reliability).
💡Expected ATG4A appearanceA credible positive is cell-associated cytoplasmic chromogen in HPA High cells such as colon glands or kidney tubules; isolated nuclear, membrane-only, or control-matched staining warrants investigation rather than an ATG4A-positive call (UniProt Q8WYN0: Cytoplasm, no transmembrane segment; HPA: tissue IHC; general IHC practice).
How each factor affects the staining
Tissue and cell selectionHPA reports High staining in appendix, colon, duodenum, and gallbladder glandular cells; kidney tubular cells; esophageal squamous cells; bone-marrow hematopoietic cells; and lymph-node germinal-center cells (HPA: tissue IHC). Choose an identifiable reported cell population for a positive comparison, while retaining HPA's Uncertain reliability qualification (HPA: tissue IHC reliability).
Compartment and topologyUniProt places ATG4A in the cytoplasm and annotates no transmembrane segment (UniProt Q8WYN0). Use a cytoplasmic scoring region in IHC; a purely nuclear or membrane-rim pattern needs independent confirmation (UniProt Q8WYN0; general IHC practice). Topology alone does not predict how paraffin processing affects staining.
Isoforms and antibody recognitionUniProt lists 4 ATG4A isoforms (UniProt Q8WYN0). The supplied sources do not map an IHC epitope to those isoforms, so a staining difference cannot be assigned to one isoform from this evidence. Keep antibody identity consistent across compared sections (general IHC practice).
IHC evidence strengthHPA labels tissue IHC reliability Uncertain, pending external verification (HPA: tissue IHC reliability). Its antibody HPA036374 has Uncertain IHC status, while HPA064759 has Approved ICC status (HPA: antibody validation). ICC approval does not upgrade the tissue IHC result; corroborate an important IHC finding independently.
IF/ICC Q&AQ: Should IF show the same pattern as paraffin IHC? A: HPA reports mainly microtubules and additional actin filaments in ICC-IF, with Approved locations; UniProt gives the broader Cytoplasm annotation (HPA: subcellular ICC-IF; UniProt Q8WYN0). Interpret IF on its own guide page and do not use filament staining as a required IHC criterion.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Reported High tissue is blank, including the run's positive-control section.The run may have failed at antibody application, retrieval, detection, or chromogen development (general IHC practice).Check reagent application and expiry, the recorded dilution, retrieval settings, and detection sequence; repeat with a documented positive-control section (general IHC practice). Colon glands or kidney tubules are reported High, although HPA tissue IHC reliability is Uncertain (HPA: tissue IHC).
Only the study specimen is blank; the positive-control section stains.The specimen may differ biologically or technically from the control; absence alone does not distinguish those possibilities (general IHC practice).Confirm target-cell preservation and section quality, then repeat alongside the positive control using the same run conditions (general IHC practice). Compare like cell types; HPA reports Low staining in several tissues and Uncertain tissue IHC reliability (HPA: tissue IHC).
Nuclear or membrane-rim staining dominates the slide.The observed compartment conflicts with cytoplasmic ATG4A and its lack of a transmembrane segment (UniProt Q8WYN0).Check localization against morphology and the no-primary control; seek independent confirmation before scoring it as ATG4A (general IHC practice). Do not reinterpret the HPA ICC-IF filament pattern as nuclear or membrane-rim IHC staining (HPA: subcellular ICC-IF).
Adipocytes or ovarian stromal cells stain more strongly than expected-positive cells.These cell types are Not detected in the HPA tissue observations; cross-reactivity or detection background is possible (HPA: tissue IHC; general IHC practice).Inspect the no-primary control and compare cell-specific signal with a reported High population in the same staining run (general IHC practice; HPA: tissue IHC). Treat the discrepancy as a reason to verify the assay, not as proof of a biological change.
Brown signal appears in the no-primary control.Signal without primary antibody points to a detection or tissue-background contribution rather than primary-dependent staining (general IHC practice).Review endogenous enzyme blocking, secondary detection, chromogen timing, and wash steps; correct the source before scoring the test slide (general IHC practice). HPA's ATG4A tissue pattern does not validate control-positive chromogen (HPA: tissue IHC profile).
Diffuse haze or uneven edge staining makes cellular scoring unreliable.Nonuniform handling, inadequate washing, or excessive detection development can produce spatial background (general IHC practice).Compare the no-primary control, inspect section coverage and wash steps, and adjust development using run controls (general IHC practice). Score only interpretable, cell-associated cytoplasmic signal; HPA reports general cytoplasmic expression but Uncertain IHC reliability (HPA: tissue IHC).

Sample controls for ATG4A IHC & IF

🧪Run colon first and require staining in glandular cells (HPA: High in colon glandular cells). Use adipose tissue adipocytes as the negative tissue (HPA: Not detected in adipocytes); on the colon slide, compare stained glands with neighboring cells that show no signal, without assuming those cells are ATG4A-negative.
Positive control tissue: Appendix (Glandular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show ATG4A in MCF-7, PC-3, U2OS, with annotated localisation: Microtubules (approved) (HPA subcellular).
Technical controls: Include no-primary (secondary-only) and rabbit IgG controls matched to the primary antibody’s clonality and concentration (caption: rabbit primary and biotinylated goat anti-rabbit secondary). Confirm specificity with ATG4A knockout material; for the biotinylated secondary and SABC/DAB workflow, block endogenous peroxidase and biotin in the colon section (caption: SABC/DAB detection).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A06539-2 tissue-IHC caption does not state the fixative (caption: fixative unreported). The reported paraffin-section workflow uses heat-mediated retrieval in EDTA at pH 8.0 (caption: EDTA pH 8.0); the supplied evidence does not establish whether frozen sections or IF would be easier. Check colonic gland lumina for retained chromogen before scoring cellular staining (HPA: High in colon glandular cells; standard IHC practice).

HPA tissue IHC evidence for ATG4A

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Pending external verification.). 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
Appendix Glandular cells High Protein (IHC) HPA →
Bone marrow Hematopoietic cells High Protein (IHC) HPA →
Colon Glandular cells High Protein (IHC) HPA →
Duodenum Glandular cells High Protein (IHC) HPA →
Esophagus Squamous epithelial cells High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes Not detected Protein (IHC) HPA →
Ovary Ovarian stroma cells Not detected Protein (IHC) HPA →
Section 3

Advanced ATG4A IHC Tips

Troubleshoot ATG4A staining in paraffin sections by checking retrieval, controls, cellular localisation and scoring before interpreting chromogenic signal.

What retrieval should I try first when ATG4A staining is weak?
Use heat-mediated EDTA retrieval at pH 8.0 for ATG4A paraffin-section IHC (datasheet A06539-2). The selected image used this retrieval before overnight incubation at 4°C with 1 μg/ml primary antibody (datasheet A06539-2). If signal is weak, compare retrieval heating and cooling conditions on matched sections while keeping antibody concentration and detection constant (standard IHC practice). Include a no-primary control and a tissue with expected glandular-cell staining, such as colon (HPA: High in colon glandular cells). Assess whether stronger signal retains a predominantly cytoplasmic pattern before accepting the adjusted retrieval (UniProt Q8WYN0: cytoplasm; HPA: general cytoplasmic expression).
Could fixation explain variable ATG4A staining between paraffin blocks?
ATG4A-specific sensitivity to fixation is unknown because the selected paraffin-section caption does not state its fixative (datasheet A06539-2). Record each block’s fixative and processing history, then compare similarly handled sections under identical retrieval and staining conditions (standard IHC practice). Start with heat-mediated EDTA at pH 8.0 and 1 μg/ml primary antibody, the conditions documented for the selected image (datasheet A06539-2). Check whether weak areas coincide with uneven morphology or staining of other antigens before attributing them to ATG4A loss (standard IHC practice). Do not infer fixation tolerance from tissue expression or the protein’s lack of a transmembrane segment (HPA: tissue profile; UniProt Q8WYN0: topology).
How should I judge punctate or nuclear ATG4A staining in IHC?
Expect predominantly cytoplasmic staining in paraffin-section IHC (UniProt Q8WYN0: cytoplasm; HPA: general cytoplasmic expression). HPA reports microtubule localisation with additional actin-filament localisation in its subcellular data, but its tissue-IHC reliability is Uncertain (HPA: subcellular summary; HPA: tissue reliability). Examine punctate staining within intact cytoplasm against matched no-primary sections and neighbouring cells before assigning a biological pattern (standard IHC practice). Strong isolated nuclear colour warrants checking counterstain, precipitate and detection background because a nuclear location is absent from the supplied localisation records (UniProt Q8WYN0: cytoplasm; HPA: subcellular summary). Capture representative fields under one staining workflow so unusual patterns can be reviewed consistently (standard IHC practice).
Can this antibody distinguish ATG4A isoforms or reveal its epitope?
The supplied record lists 4 ATG4A isoforms, but the selected IHC caption does not identify the antibody’s epitope or isoform coverage (UniProt Q8WYN0: isoforms; datasheet A06539-2). Treat chromogenic signal as antibody-reactive ATG4A unless independent epitope information and isoform-specific validation become available (standard IHC interpretation). ATG4A has no annotated transmembrane segment, signal peptide, propeptide or glycosylation sites, which does not establish antibody access to a particular epitope (UniProt Q8WYN0: topology and processing). Compare staining with an orthogonal expression measure or a validated loss-of-target control when isoform attribution matters (standard IHC practice). Keep retrieval and detection conditions constant across those comparisons (standard IHC practice).
How can IF help assess a questionable ATG4A IHC pattern?
Use IF as a separate localisation check, selecting a marker for the expected cell population when comparing it with chromogenic IHC (standard IF practice). For example, colon glandular cells show High tissue-IHC expression, although HPA rates its tissue-IHC evidence Uncertain (HPA: colon glandular cells; HPA: tissue reliability). Choose fluorophores in channels with low tissue autofluorescence and include single-stain controls for multiplex imaging (standard IF practice). Because ATG4A is cytoplasmic and has no transmembrane segment, permeabilise the plasma membrane to access its cytoplasmic epitope; the epitope itself is unspecified here (UniProt Q8WYN0: cytoplasm and topology; datasheet A06539-2). Compare IF localisation with IHC cautiously because the supplied caption documents paraffin-section IHC conditions, not IF validation (datasheet A06539-2).
What should I check when brown signal obscures ATG4A staining?
Run a no-primary section to assess staining from secondary and chromogenic detection, and inspect unstained tissue for endogenous pigment (standard IHC practice). Block endogenous peroxidase before DAB development and check for endogenous biotin when using the documented biotinylated secondary and streptavidin-biotin complex (standard IHC practice; datasheet A06539-2: detection system). The selected image used 10% goat serum blocking and 1 μg/ml rabbit primary antibody overnight at 4°C (datasheet A06539-2). Compare background after adjusting washing or blocking while holding retrieval and exposure conditions fixed (standard IHC practice). Distinguish diffuse chromogen or section-edge staining from cytoplasmic signal within intact cells (UniProt Q8WYN0: cytoplasm; standard IHC practice).
How should I quantify ATG4A across paraffin-section samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and tissue area before scoring ATG4A chromogenic staining (standard IHC practice). An H-score combines the percentage of cells at each intensity into a 0–300 score; alternatively report percent positive cells or positive-cell density per mm² (standard IHC scoring practice). Normalise counts to viable tissue area or the number of evaluable cells in the same compartment, excluding folds and necrosis (standard IHC practice). Score cytoplasmic staining separately from nuclear colour because supplied localisation evidence places ATG4A in the cytoplasm (UniProt Q8WYN0: cytoplasm; HPA: general cytoplasmic expression). Apply one threshold, retrieval condition and imaging setup across samples, and report HPA tissue-IHC reliability as Uncertain when using its pattern as context (standard IHC practice; HPA: tissue reliability).
How do I separate plausible ATG4A signal from artefact?
Look for staining within intact cytoplasm, the supplied location for ATG4A, rather than treating every brown deposit as positive (UniProt Q8WYN0: cytoplasm; standard IHC practice). HPA reports High staining in colon glandular cells and no detection in adipocytes, but labels its tissue-IHC reliability Uncertain (HPA: tissue profile and reliability). Use those patterns as context alongside matched controls, not as proof that an individual section is specific (standard IHC interpretation). Exclude section-edge gradients, necrotic regions, pigment and signal reproduced on no-primary sections before scoring (standard IHC practice). Check endogenous peroxidase and, with the documented streptavidin-biotin detection, endogenous biotin when background persists (standard IHC practice; datasheet A06539-2: detection system).
Boster reagents

Best ATG4A / Cysteine protease ATG4A IHC Antibodies

The catalog includes ATG4A antibodies with human tissue IHC images (catalog IHC captions) and an IF image in human cells (M06539-1 IF caption); listed reactivity also includes mouse and rat (A06539 catalog).

Real IHC data IHC analysis of ATG4A using anti-ATG4A antibody (A06539-2). ATG4A was detected in paraffin-embedded section of human rectal cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1μg/ml rabbit anti-ATG4A Antibody (A06539-2) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1022) with DAB as the chromogen.
Anti-ATG4A Antibody ®
Cat # A06539-2
Real IHC data M06539-1 staining ATG4A in human brain sections by Immunohistochemistry (IHC-P -paraformaldehyde-fixed, paraffin-embedded sections). Tissue was fixed with formaldehyde and blocked with 3% BSA for 0. 5 hour at room temperature; antigen retrieval was by heat mediation with a citrate buffer (pH6). Samples were incubated with primary antibody (1/25) for 1 hours at 37°C. A undiluted biotinylated goat polyvalent antibody was used as the secondary antibody.
Anti-ATG4A Antibody
Cat # M06539-1
Real IHC data Immunohistochemistry of ATG4A in human spleen tissue with ATG4A antibody at 5 μg/ml.
Anti-Cysteine protease ATG4A ATG4A Antibody
Cat # A06539

A06539-2 shows IHC in human rectal cancer paraffin sections (A06539-2 IHC caption); M06539-1 shows IHC in formaldehyde-fixed human brain paraffin sections (M06539-1 IHC caption). A06539 shows IHC in human spleen tissue (A06539 IHC caption), while M06539-1 also shows IF in paraformaldehyde-fixed, permeabilized HeLa cells (M06539-1 IF caption).

Which to pick: For human paraffin-section IHC, A06539-2 has an image using EDTA retrieval and 1 μg/mL primary antibody; its fixative is unreported (A06539-2 IHC caption). For IF/ICC, choose mouse monoclonal M06539-1: IF is listed at 1:25 and illustrated in HeLa cells; its separate IHC image documents paraffin-section brain sections with citrate retrieval (M06539-1 catalog; M06539-1 IF and IHC captions). For mouse or rat studies, A06539 lists those species as reactive, but its pictured IHC validation is in human spleen, so verify IHC performance in the intended species (A06539 catalog; A06539 IHC caption). The selected A06539-2 tissue-IHC caption documents paraffin sections, but does not specify the fixative (selected-SKU IHC image A06539-2).

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

References

  1. UniProt Consortium. UniProt entry Q8WYN0 (ATG4A_HUMAN, Cysteine protease ATG4A).
  2. Human Protein Atlas. ATG4A tissue IHC expression (reliability: Uncertain).
  3. Human Protein Atlas. ATG4A subcellular location (ICC-IF): Mainly localized to the microtubules. In addition localized to the actin filaments..
  4. Human Protein Atlas. ATG4A antibody validation summary (2 antibodies).
  5. ATG4A promotes tumor metastasis by inducing the epithelial-mesenchymal transition and stem-like properties in gastric cells. Oncotarget 2016 — PMC5129932.
  6. Exploring the interplay between EBV and autophagy-related gene expression patterns in nasopharyngeal carcinoma. Frontiers in oncology 2025 — PMC12234470.
  7. A mammosphere formation RNAi screen reveals that ATG4A promotes a breast cancer stem-like phenotype. Breast cancer research : BCR 2013 — PMC3978845.
  8. Predisposition to cortical neurodegenerative changes in brains of hypertension prone rats. Journal of translational medicine 2023 — PMC9881299.
  9. PubMed PMID:12446702 — UniProt-cited evidence.
  10. PubMed PMID:30808002 — UniProt-cited evidence.
  11. PubMed PMID:15169837 — UniProt-cited evidence.