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CTSE / Cathepsin E · IHC design guide
Design Immunohistochemistry for CTSE
Plan CTSE IHC in paraffin sections using stomach glandular cells as a high-staining reference (HPA tissue IHC). This guide covers fixation consistency, controls and interpretation of cytoplasmic and membranous tissue staining (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CTSE Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Cytoplasmic and membranous tissue staining (HPA tissue IHC) | |
| Staining pattern | Stomach glandular cells show cytoplasmic and membranous staining (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet A04874-1) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A04874-1) | |
| Caveat | Intestinal staining favors endocrine cells over other cell types (HPA tissue IHC) | |
| Regulation | CTSE in activated, not resting, B cells (UniProt) | |
| Isoform / epitope | 3 isoforms; processing may remove N-terminal epitopes (UniProt) |
Section 1
Recommended CTSE IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by published CTSE staining methods for nerve and gastrointestinal tissue (PMC5460450; PMC3922809).
| Sample | Paraffin-embedded human Lung cancer tissue; fixative not specified (datasheet A04874-1) |
| Fixation | Image fixative and duration unreported (datasheet A04874-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet A04874-1) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A04874-1) |
| Primary antibody | Rabbit anti-CTSE, 2μg/ml (datasheet A04874-1) |
| Primary incubation | Overnight at 4 °C (datasheet A04874-1) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A04874-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CTSE-positive staining in endocrine cells of appendix (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic and membranous expression most abundant in stomach but also in intestine, gallbladder, urinary bladder and squamous epithelia of tonsil. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated citrate pH 6 retrieval for the catalog antibody (datasheet A04874-1). The colonic biopsy study did not specify which of its two buffers was used for CTSE (PMC3922809).
Section 2
What Is the Expected CTSE Staining Pattern?
CTSE is an endosomal protein; its proenzyme localizes to the ER and Golgi, and it has no transmembrane segment (UniProt P14091). In tissue IHC, expect cytoplasmic and membranous staining, especially in stomach glandular cells and intestinal endocrine cells (HPA: High). HPA rates the tissue pattern Enhanced, with medium consistency between staining and RNA expression (HPA: tissue IHC).
| Strong staining in stomach glandular cells, with cytoplasmic and membranous signal (HPA: High; tissue IHC). | This is the clearest tissue-positive pattern in the supplied record. CTSE is most abundant in stomach by HPA IHC; the mature enzyme localizes to endosomes (HPA: tissue IHC; UniProt P14091). |
| Staining in scattered endocrine cells of appendix, duodenum or rectum (HPA: High). | A restricted cell population can be a correct positive result. Score the named endocrine cells, rather than assuming every epithelial cell should stain (HPA: tissue IHC). |
| Predominantly nuclear staining, without the expected cytoplasmic pattern. | Treat this as a compartment mismatch requiring validation, since HPA reports cytoplasmic and membranous tissue staining and UniProt places CTSE in the secretory pathway and endosomes (HPA: tissue IHC; UniProt P14091). |
| Strong signal in adipocytes or bronchial respiratory epithelial cells (HPA: Not detected). | Check for cross-reactivity or endogenous detection activity before interpreting it as CTSE. HPA reports no detection in these specific cell types; that does not make their entire tissues universal negative controls (HPA: tissue IHC). |
| Diffuse staining across cells and surrounding section, or no signal in stomach glandular cells. | Diffuse signal warrants a background check; absent stomach signal warrants a run-performance check. The expected cell-restricted, high stomach pattern supplies the comparison, but HPA does not identify the technical cause (HPA: tissue IHC). |
💡Expected CTSE appearanceCall a section positive when stomach glandular cells show strong cytoplasmic and membranous staining, or the named intestinal endocrine cells stain strongly; isolated nuclear signal or uniform background is suspect (HPA: High; tissue IHC; UniProt P14091).
| Tissue and cell choice (HPA: tissue IHC) | Stomach glandular cells are High; appendix, duodenum and rectum endocrine cells are also High. Gallbladder glandular cells are Medium, so compare like cell types when judging intensity (HPA: tissue IHC). |
| Compartment and processing (UniProt P14091) | The proenzyme localizes to ER and Golgi, while mature CTSE localizes to endosomes. CTSE has a signal peptide and propeptide; a compartment shift alone cannot identify which processed form an unspecified antibody detects (UniProt P14091). |
| Antibody evidence (HPA: antibody validation) | HPA012940 and CAB032687 have Enhanced IHC status, meaning the pattern is supported by independent antibodies or orthogonal data. HPA also reports medium staining–RNA consistency; neither statement validates every antibody or specimen (HPA: antibody validation; tissue IHC). |
| IF/ICC: what pattern is expected? (HPA: subcellular) | HPA reports approved vesicular localization in ICC-IF, with images from OE19 and U2OS. Use that as an IF localization reference; tissue IHC reports cytoplasmic and membranous staining (HPA: subcellular; tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| No staining in stomach glandular cells (HPA: High). | The run may have failed; the supplied sources do not establish CTSE-specific fixation or retrieval sensitivity. | Check section integrity, reagent performance and a known-positive stomach section. Review retrieval using general IHC practice, without assuming a CTSE-specific retrieval condition (HPA: tissue IHC). |
| Only nuclei stain. | The observed compartment conflicts with HPA tissue staining and UniProt localization (HPA: tissue IHC; UniProt P14091). | Compare a stomach positive section and a detection-only control; reassess antibody specificity before scoring nuclear signal as CTSE (HPA: High in stomach glandular cells). |
| Adipocytes stain strongly (HPA: Not detected). | Cross-reactivity or endogenous detection activity is possible; HPA alone cannot distinguish them. | Inspect a detection-only control and compare the signal with CTSE-positive glandular cells in stomach (HPA: High; tissue IHC). |
| Brown signal spreads uniformly beyond cell boundaries. | Background from blocking, washing or detection can obscure the cell-restricted pattern; the cause is not established by HPA. | Check a detection-only control and optimize blocking and washes using standard IHC practice. Score only interpretable cellular staining against the HPA tissue pattern (HPA: tissue IHC). |
| Weak staining in lung or bone marrow. | HPA reports Low staining in lung alveolar type II cells and bone marrow hematopoietic cells; weak signal there need not indicate failure (HPA: tissue IHC). | Compare with a stomach glandular-cell positive section before changing detection conditions (HPA: High in stomach glandular cells). |
| Staining differs between intestinal cells. | HPA reports High staining in named endocrine cells but does not assign that level to all intestinal cells (HPA: tissue IHC). | Identify the scored cell population and compare it with the corresponding HPA cell type; investigate widespread staining separately (HPA: tissue IHC). |
Experiment evidence
IHC & IF images showing CTSE staining
A04874-1 · IHCIHC analysis of Cathepsin E using anti-Cathepsin E antibody (A04874-1). Cathepsin E was detected in paraffin-embedded section of human Lung
A04874-1 · IHCIHC analysis of Cathepsin E using anti-Cathepsin E antibody (A04874-1). Cathepsin E was detected in paraffin-embedded section of human gastr
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000196188-CTSE/tissue/cerebral+cortex#imid_15927444
HPA · StomachHuman Protein Atlas IHC, Stomach. Source: https://www.proteinatlas.org/ENSG00000196188-CTSE/tissue/stomach+2#imid_15927328
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000196188-CTSE/tissue/colon#imid_15927370
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000196188-CTSE/tissue/liver#imid_15927379
HPA · ICC-IF OE19Human Protein Atlas immunofluorescence, OE19, antibody HPA012674; green = CTSE, blue = nucleus, red = microtubules.
HPA · ICC-IF OE19Human Protein Atlas immunofluorescence, OE19, antibody HPA012674; green = CTSE, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CTSE IHC & IF
🧪Run stomach first: glandular cells should stain (HPA: High in stomach glandular cells). Use adrenal glandular cells as the negative tissue (HPA: Not detected in adrenal glandular cells); on the stomach slide, adjacent background and nonglandular structures should lack specific chromogenic signal (HPA: High is assigned to glandular cells).
Positive control tissue: Appendix (Endocrine cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CTSE in OE19, U2OS, with annotated localisation: Vesicles (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and a concentration-matched rabbit isotype control (caption: rabbit primary antibody), plus CTSE-knockout tissue as a biological specificity control (standard IHC practice). Block endogenous peroxidase and check for endogenous biotin signal in stomach sections because the selected detection uses a biotinylated secondary, streptavidin–biotin complex and DAB (caption: A04874-1).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected SKU’s paraffin-section caption does not state the fixative (caption: A04874-1). The demonstrated IHC procedure uses heat retrieval in citrate buffer at pH 6 for 20 minutes (caption: A04874-1); whether frozen sections or IF are easier is unreported, although ICC-IF images show vesicular localization (HPA: Vesicles, approved). In stomach, assess glandular luminal background against the negative controls when scoring (HPA: High in stomach glandular cells; standard IHC practice).
HPA tissue IHC evidence for CTSE
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 |
|---|---|---|---|---|
| Appendix | Endocrine cells | High | Protein (IHC) | HPA → |
| Duodenum | Endocrine cells | High | Protein (IHC) | HPA → |
| Rectum | Endocrine cells | High | Protein (IHC) | HPA → |
| Stomach | Glandular cells | High | Protein (IHC) | HPA → |
| Colon | Endocrine cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced CTSE IHC Tips
Troubleshoot CTSE staining in paraffin sections by checking retrieval, cell identity and compartment before comparing chromogenic signal across samples.
What retrieval should I try first when CTSE staining is weak?
Begin with heat mediated retrieval in citrate buffer at pH 6 for 20 minutes (datasheet A04874-1). Keep the antibody incubation and detection steps constant while comparing retrieved and unretrieved sections, so the effect of retrieval is interpretable (standard IHC practice). The documented paraffin section workflow used 2 µg/mL antibody overnight at 4°C after retrieval (datasheet A04874-1). If staining remains weak, adjust heating duration cautiously and check tissue integrity before testing another buffer as a fallback (standard IHC practice). Include stomach glandular cells as a positive reference when available (HPA: High in stomach glandular cells).
Could fixation explain inconsistent CTSE staining between paraffin blocks?
CTSE specific sensitivity to fixation is unknown because the supplied tissue caption does not state a fixative (datasheet A04874-1: fixative not stated). Record each block’s fixative and processing history, then compare sections using the same citrate retrieval at pH 6 for 20 minutes (datasheet A04874-1; standard IHC practice). Use matched section thickness, antibody incubation and detection conditions when assessing whether the difference follows the block rather than the staining run (standard IHC practice). A weak block cannot be diagnosed as overfixed from its appearance alone; inspect morphology and include a known positive reference section in the same run (standard IHC practice).
Where should convincing CTSE staining appear in a tissue section?
Expect intracellular staining compatible with the endosomal location of mature CTSE; its proenzyme is localized to the endoplasmic reticulum and Golgi apparatus (UniProt P14091: subcellular location). HPA reports cytoplasmic and membranous tissue staining, most abundant in stomach, while its subcellular images assign CTSE to vesicles (HPA: tissue profile; HPA: vesicles). Assess signal within identified cells against a counterstain, rather than treating a diffuse deposit across empty spaces as cellular staining (standard IHC practice). Compare the pattern with a stomach glandular cell reference processed using citrate retrieval at pH 6 for 20 minutes (HPA: High in stomach glandular cells; datasheet A04874-1).
Can this antibody distinguish mature CTSE from precursor or splice isoforms?
Do not assign a staining pattern to one CTSE form without an antibody epitope map or form specific validation (standard IHC interpretation). The annotated precursor has a signal peptide at residues 1–19 and propeptide at 20–53; mature chains begin at 54 or 57 (UniProt P14091: processing). UniProt lists 3 isoforms and one glycosylation site at residue 90, so epitope coverage and accessibility require checking against the antibody documentation (UniProt P14091: isoforms and glycosylation; standard IHC practice). Keep retrieval at citrate pH 6 for initial comparisons and describe the result as CTSE immunoreactivity until specificity is established (datasheet A04874-1; standard IHC interpretation).
How should I assess CTSE localisation by IF alongside a cell identity marker?
Treat IF as a separately optimised application: the supplied antibody caption documents chromogenic staining of a paraffin section, with citrate retrieval at pH 6, rather than an IF procedure (datasheet A04874-1). Multiplex CTSE with a validated marker for the expected cell population and compare intracellular puncta with HPA’s vesicular localisation (HPA: vesicles; standard IF practice). Choose fluorophores after inspecting tissue autofluorescence and include single stain controls to check spectral overlap (standard IF practice). For intracellular epitopes, optimise permeabilisation to allow antibody access to the relevant side of the organelle membrane; CTSE has no annotated transmembrane segment, but the supplied evidence does not map this antibody’s epitope (UniProt P14091: topology; standard IF practice).
How can I reduce diffuse or granular DAB background without losing CTSE signal?
First compare a no primary control with the stained section to identify signal produced by detection reagents rather than the CTSE antibody (standard IHC practice). For the documented method, retain the 10% goat serum block initially and review whether background tracks the biotinylated secondary or streptavidin–biotin detection system (datasheet A04874-1; standard IHC practice). Apply a peroxidase block before DAB development, and check endogenous biotin controls if background persists with this detection system (standard chromogenic IHC practice). Titrate incubation or detection intensity only after controls are reviewed, using a stomach glandular cell section to monitor loss of expected signal (HPA: High in stomach glandular cells; standard IHC practice).
What should I score when CTSE staining varies across cell types? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and region before scoring, because HPA reports High staining in stomach glandular cells and endocrine cells in several intestinal tissues (HPA: tissue IHC). Within that population, record percentage of positive cells and intensity on a 0–3 scale, or calculate an H-score on a 0–300 scale (standard IHC scoring practice). Normalise counts to the number of eligible cells, or report positive cell density per mm² of viable tissue when cell counts are impractical (standard IHC scoring practice). Exclude necrotic and damaged edges consistently, and keep citrate retrieval at pH 6 comparable across samples (standard IHC practice; datasheet A04874-1).
How do I separate true CTSE staining from tissue or detection artefacts?
A credible signal should align with identified cells and an intracellular pattern consistent with endosomal CTSE, while allowing for proenzyme in the endoplasmic reticulum and Golgi apparatus (UniProt P14091: subcellular location). Compare cell identity with reference patterns: stomach glandular cells stain High, whereas bronchial respiratory epithelial cells are reported as not detected (HPA: tissue IHC). Suspect an artefact when DAB accumulates at section edges, in necrotic regions or in a no primary control; assess endogenous peroxidase and biotin contributions to the documented detection system (datasheet A04874-1; standard IHC practice). The lung cancer image demonstrates staining under citrate pH 6 retrieval, but does not establish that every lung cell is CTSE positive (datasheet A04874-1; HPA: lung alveolar type II cells Low).
Boster reagents
Best CTSE / Cathepsin E IHC Antibodies
The IHC-validated CTSE antibody A04874-1 has images from human lung and gastric cancer paraffin sections (catalog IHC captions). Human, mouse and rat reactivity is listed; IF data are unreported (catalog reactivity/images).
Real IHC data
Anti-Cathepsin E/CTSE Antibody ®
Cat # A04874-1
A04874-1 has IHC images from human lung cancer and gastric cancer paraffin sections (catalog IHC captions). Its listed application is IHC, with human, mouse and rat reactivity; IF/ICC validation is unreported (catalog applications/reactivity/images).
Which to pick: Choose A04874-1 for paraffin-section tissue IHC: it is a rabbit polyclonal antibody, and its IHC captions document human lung and gastric cancer sections (catalog host/clonality; catalog IHC captions). No SKU in this payload has reported IF/ICC validation (catalog applications/images). For cross-species work, A04874-1 lists mouse and rat reactivity, but the supplied IHC images show human sections only; the fixative is unreported (catalog reactivity; catalog IHC captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P14091 (CATE_HUMAN, Cathepsin E).
- Human Protein Atlas. CTSE tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. CTSE subcellular location (ICC-IF): Localized to vesicles..
- Human Protein Atlas. CTSE antibody validation summary (3 antibodies).
- Monitoring pancreatic carcinogenesis by the molecular imaging of cathepsin E in vivo using confocal laser endomicroscopy. PloS one 2014 — PMC4153675.
- CTSE Overexpression Is an Adverse Prognostic Factor for Survival among Rectal Cancer Patients Receiving CCRT. Life (Basel, Switzerland) 2021 — PMC8304221.
- Differential expression of Cathepsin E in transthyretin amyloidosis: from neuropathology to the immune system. Journal of neuroinflammation 2017 — PMC5460450.
- RNA sequencing of sessile serrated colon polyps identifies differentially expressed genes and immunohistochemical markers. PloS one 2014 — PMC3922809.
- PubMed PMID:2674141 — UniProt-cited evidence.
- PubMed PMID:1370478 — UniProt-cited evidence.
- PubMed PMID:7983070 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CTSE (Cathepsin E). Expected localisation Cytoplasmic and membranous tissue staining (HPA tissue IHC). Antigen retrieval: Citrate pH 6 HIER, heat-mediated (datasheet A04874-1). Validated IHC antibody: A04874-1 at 2μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Appendix (Endocrine cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human Lung cancer tissue; fixative not specified (datasheet A04874-1); 2. Fixation: Image fixative and duration unreported (datasheet A04874-1); 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: Citrate pH 6 , 20 min (datasheet A04874-1); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A04874-1); 8. Primary antibody: Rabbit anti-CTSE, 2μg/ml (datasheet A04874-1); 9. Primary incubation: Overnight at 4 °C (datasheet A04874-1). Watch for: Fixation: Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A04874-1); Caveat: Intestinal staining favors endocrine cells over other cell types (HPA tissue IHC); Isoform / epitope: 3 isoforms; processing may remove N-terminal epitopes (UniProt); Regulation: CTSE in activated, not resting, B cells (UniProt). Evidence: UniProt P14091, HPA tissue IHC · Enhanced, HPA ICC-IF · vesicles., Datasheet A04874-1, PMC5460450, PMC3922809. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CTSE/immunohistochemistry-ihc-guide.